Sage 50 automatically will track QHSF, you can change its factor from Setup > Settings > Payroll > Taxes. But the program does not have a feature to automatically calculate and track CNT contribution for now. Because it is an employer contribution the calculation needs to be embedded in the program so it does the calculaltion on each paycheque (transactions will be in the journal entry of the paycheque not in the paystub).
For the pay remittance yes you can manually adjust from Remittance Payment screen. But when the QHSF remittance is setup it will automatically show the amount to remit. Please click on the following link to setup a remittance.
260-20022 - How to set up Payroll Remittance
You can also create an employer expense for CNT, it is called user defined expense in the program. That way you can then setup a remittance for that employer expense. If the contribution does not change from paycheque to paycheque there is an option to setup a fixed amount. You can manually enter the contribution payment under Paycheque screen as the program cannot calculate it automatically. One more thing to know about the user defined expense is that there is no payroll deduction calculated on it. Please find below instructions on how to setup a user defined expense.
260-19697 - User defined expenses in Sage 50 Canada
Hope this could help