Welcome to the QuickBooks Online community! I can help you with recording your late remittance penalty to the CRA.
Although the penalty is related to your payroll, the fee itself isn't part of the payroll tax calculations. Because of this, these kinds of fees get recorded outside of the payroll tax module as a regular cheque or expense. Here's how you would do it: create a cheque or expense through the create + icon. You can also set up the CRA as a supplier if you'd like, but this is optional. Both transactions will allow you to save without having a supplier listed.
Enter a cheque or expense for the late fee
Choose from one of the following methods to enter the late fee transaction.