Shareholder payback through payroll

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Hi,  My accountant wants me to do some bonuses for an owner/shareholder to virtually pay back the money they borrowed.  The shareholder already receives a monthly salary so this would be in addition to their existing salary.  The shareholder will not receive any money but the payroll taxes would need to be deducted and remitted.  What is the best way to do this?  Do I need to account for CPP?  Should I just enter a monthly payroll bonus on a separate cheque  and then do a journal entry to debit the bank and credit the Shareholders Loan?  OR should I enter a bonus on the same monthly cheque and then do the journal entry.  Basically will paying the bonus on the same cheque affect the taxes or will it all work out?