Record a GST/HST payment from the bank line

A payment to the CRA for GST/HST is not an expense. It settles the tax owing your books are already carrying, so it clears your sales-tax account instead of adding a cost. Booking it as an expense overstates your costs, and the amount owing stays on your books as if it was never paid.

The payment is sitting on your bank feed or statement

When the withdrawal is already in Ledger › Banking › Transactions, record it from the line itself:

Mark the period as filed first, on Ledger › Reports › Tax › GST/HST. Filing is what establishes the amount owing that the payment settles.
Open the withdrawal's details with the arrow at the right of the row, and look under "Not what it looks like?".
Choose Tax payment, pick the filed period, and pick the regime (GST/HST, or QST if you remit both on the combined Quebec filing). The period whose balance owing is exactly this withdrawal is marked matches this return (matches the books' figure when TALISK_HQ has no copy of the return). Picking a different one while another matches gets a note, never a refusal: interest or an offset can make the two differ.
Confirm with OK. TALISK_HQ posts one entry that reduces the tax owing and takes the money out of the bank account the line belongs to. The line shows a "Tax paid" pill and stops reading as uncategorized. Its Category column names the account the payment cleared (GST/HST Payable (net), or QST Payable (net)) in grey italics. That is not a category to fill in: the payment entry already booked it.

If you already recorded the payment on the GST/HST tab, marking the bank line does not create a second entry: TALISK_HQ finds the recorded payment and attaches it to the line, moving its cash side onto that bank account. If the recorded amount differs from the withdrawal, TALISK_HQ refuses and tells you the recorded figure, because a mismatch usually means installments or added interest, and those belong in a manual journal entry where you can see them.

Dates TALISK_HQ checks

The payment's date is the withdrawal's own date on a bank line, and the date you type on the GST/HST tab.

Before the period starts. Paying a return before its period begins is rare, so TALISK_HQ asks first: check you picked the right period, then tick It's a prepayment for this period, so record it anyway. The first day of the period asks nothing.
Before your conversion date, the day your TALISK_HQ books begin. TALISK_HQ refuses: that money is already in your opening balances, so there is nothing to record. Correct the opening balances on Ledger › Accounting › Opening Balances if they are wrong. Paying a period that ended before your conversion date, on or after that date, is fine.

The payment was recorded on the GST/HST tab only

That is still correct bookkeeping: the entry exists and the worksheet shows the period as paid. But if the withdrawal later arrives on a bank feed or statement, it will sit uncategorized. Use the steps above on that line and TALISK_HQ will adopt the recorded payment rather than posting a twin.

A payment you already booked by hand

Both places check before they record anything, and say so: the GST/HST tab's Record payment / refund dialog, and the Tax payment picker on the bank line once you pick a GST/HST or QST period. The check looks for:

A journal entry posted by hand that already pays the tax owing.
A bank withdrawal of exactly the payment amount, dated on or after the period started, that is already categorized to another account. That withdrawal is the money already in your books.
On the bank line only: an entry that moves the account the withdrawal is coded to the opposite way, by exactly the payment amount. That is a payment moved out of a suspense account by hand through some other account.

Each lists the entries with their date, the amount, the other accounts they touch, and flags one of the same amount. View entry opens it.

If that entry is this payment, record nothing. On the bank line, leave the withdrawal as it is: marking it would clear the same tax owing a second time.
If the only record is the withdrawal itself, categorized to another account, mark that withdrawal on Ledger › Banking with Tax payment instead of recording it on the GST/HST tab. That replaces its category, so the money is booked once. When the withdrawal cannot be marked that way (a card line, a foreign currency line, or one already matched), the dialog says so, and the fix is a journal entry from your accountant.
If it paid part of the return, such as an installment, the withdrawal may be the rest. Tick I've checked and record it. In the dialog, change the amount to what is still owed first, unless line 113 already took it off (below).
If it is something else, tick I've checked and record the payment.

The amount the dialog fills in is line 113 of the return, the balance after the installments on line 110. An entry the dialog lists that is one of those line 110 installments is therefore not a reason to change the amount: tick I've checked and record it as it stands. An installment you did not enter on line 110 is not in line 113, so take that one off. On an annual return the dialog also says that TALISK_HQ records no QST installments: for QST the amount is the whole year's net tax, so change it to the balance after any you paid.

The withdrawal's own category is never listed: marking the line replaces it. If another bank line holds the same withdrawal (it was imported twice) and that line is categorized, the picker lists it too. Remove the duplicate before you mark. A PST remittance settles no filing period, so the PST branch asks nothing.

The check cannot see a withdrawal that is not exactly the payment, or a clearing entry that moved the money through an income or expense account. The bank line also refuses a payment when another filing period with the same dates already has one recorded. Only older books can hold that, and the message names the payment that is already there.

The check also runs the other way round. The New Journal Entry form asks before posting an entry that would pay the same tax again, and Move balance warns in its preview. And if a journal entry, or another withdrawal of the same amount coded to another account, turns up after the payment was recorded, the Books Health panel shows a card saying the payment may be recorded twice; A GST/HST payment or refund recorded twice explains which record to remove.

Record which entry paid it

A filed period reads GST/HST paid only once TALISK_HQ knows what settled it. When the payment is already in your books as a journal entry, link that entry instead of recording the payment again: click Link a settlement on the GST/HST tab's green Filed banner, then Link this entry on the entry that records it. TALISK_HQ lists only the entries that already pay down GST/HST Payable (net) for that period.

The period then reads GST/HST paid on that entry's date, marked journal entry, with View entry beside it. Nothing is posted and the entry is not changed. While it is linked, Record payment / refund and the bank line's Tax payment both refuse that period and name the entry, and Record payment / refund on any other period stops listing it. Unlink beside the pill undoes it, and TALISK_HQ records who unlinked it and when. If the entry is deleted, reversed, or changed so it no longer pays down the net tax account by the same amount, the period reads unpaid again by itself.

When the entry's amounts differ from the return's payment, or it pays down more than this return, TALISK_HQ asks you to confirm before linking it: once linked, another period's Record payment / refund no longer asks about it, so link it only if it is this return's payment. If one payment covered more than one return (two quarters paid together), split it into one journal entry per return and link each to its own return. An entry that moves the net tax account both ways (it nets one balance against another), and an entry undone by an exact reversing entry, are listed with the reason and cannot be linked.

A return for a period that ended before your conversion date was usually paid before you started using TALISK_HQ. Choose It was settled before TALISK_HQ in the same dialog: the period reads GST/HST paid before TALISK_HQ and nothing is posted. TALISK_HQ asks you to confirm first when the payment was due on or after your conversion date, or when your books already hold an entry after that date that may record it. On a Quebec book, GST/HST and QST are linked separately. Recording several past returns at once from Record past returns on GST/HST returns, you can tick Paid before TALISK_HQ on each row instead.

Undo

Open the marked line's details and choose Undo tax payment. This removes the payment entry entirely, so the period reads unpaid again, even if the payment was first recorded from the GST/HST tab. Record it again from either place.

Undo does not put back the category the withdrawal had before you marked it. Until you categorize the withdrawal again, or mark it against the right period, it posts nothing, and your books show that bank account holding money that has already left it.

Remove a payment recorded by mistake

A payment recorded with Record payment / refund can be removed whether or not the period has been filed:

On a filed period, click Remove payment beside the GST/HST paid pill on the GST/HST tab's green Filed banner, or on the period's row in Ledger › Reports › Tax › GST/HST returns.
On a period that has not been filed yet, the payment shows on the GST/HST tab just above the Adjustments box, with the same button.

A Quebec book has a separate button for the QST payment. Check the amount and date in the confirmation, and confirm. TALISK_HQ deletes the payment entry, so the period reads unpaid again. On a filed period the banner then offers Record payment / refund again, and the figures you filed do not change: the return, its GST34 worksheet and the filing entry stay exactly as they were. Nothing is sent to the CRA.

On a filed period, the button appears only where TALISK_HQ can remove the payment. It does not appear, and TALISK_HQ will not remove the payment, when:

The payment is dated inside a closed period. An entry inside a closed period is never deleted. Post a correcting journal entry dated in an open period instead.
A bank line records the payment. Use Undo tax payment on that line instead. If the line was deleted from Banking since, for example when a statement was deleted to import it again, it still claims the payment and there is no line left to undo it from: ask your accountant which record to keep.
The payment was recorded before the filing period itself existed, so it is not that period's own payment.

QST on the combined Quebec filing

A Quebec registrant remits GST and QST together, but the books track them on separate accounts. If one withdrawal covered both, record the two portions from the GST/HST + QST tab as two payments instead, and leave the bank line as it is: one bank line cannot split across two regimes yet.