We currently pay the GST remittance through online banking/CRA website. I don't have the bank account linked at this time. So I'm looking at how to book the annual remittance to show the payment applied to the accounts.
During the filing process, there is an option to check 'Paper or other filing method' or 'File online'. Choose 'Paper or other filing method'. Once you've done that another window will come up asking you to choose 'Pay now' or 'Pay later'. Either way, the net GST amount owing has now become part of your Accounts Payable ledger under your Receiver General vendor. Whether you 'Pay now' or 'Pay later', you will be using the 'Pay Bills' feature to make your remittance to CRA.