The bonuses will end up on the owner/shareholder's T4 slip at the end of the year, so you definitely need to account for CPP.  (If they're large bonuses, this will just mean that you get to the maximum annual deduction for CPP all the faster.)

In general, it is easiest to do just one cheque per pay period (month, in your case), as that is what Sage's payroll calculations assume you are doing.  For example, if you do a 2nd cheque to anyone (not just an owner/shareholder) in a pay period, you should hand-calculate the CPP - otherwise, Sage won't take enough CPP.  This is because Sage applies the per-pay-period CPP exemption to every cheque, even if there has already been a cheque this period.  

As for taxes - again, the easiest thing is to just put the bonus on their regular paycheque, but this might not be the best thing to do, as you could end up with an awful lot of tax to get to a certain amount of net pay.  I suggest touching base with your firm's accountant to see if they have any instructions for what tax deductions they are planning for.

There are two ways to deal with the 'paying off the shareholder loan' portion of this.  If it's going to happen often, and if you have a spare deduction paycode in Sage, you can set up 'shareholder loan' as a deduction on their paycheque.  Or, you can just change the 'bank' on their paycheque screen to 'wages payable' rather than your actual bank account, and then do (a) a handwritten cheque to pay their actual, ordinary net pay (general journal entry, Dr wages payable, Cr bank), and (b) a general journal entry to move the rest to shareholder loan (Dr wages payable, Cr shareholder loan.)

The question is are these actually bonuses or a repayment of a shareholder loan to the business. As C White states bonuses are taxable. A repayment back to a shareholder for monies loaned to the business is not taxable. When you know the answer, it is either a payroll transaction or a payable transaction.

Hope this helps!