Hi there,
Thanks for reaching out in the Community. Since this is your fist time posting, I'd like to give you a warm welcome! :)
If you've underpaid on your last remittance, I recommend paying the government the outstanding amounts and recording them in QuickBooks as paid after you've done that. Based on what you've described, it sounds like you're using Standard Payroll and at this time, you can't add custom amounts to your cheque with Standard Payroll.
Let me know if you have further questions. I'm here to help.
