I can't confirm this right now, but I have done this before with a construction company.  If I recall, when you use Class tracking (or Job tracking) on the different lines of your income Payroll Items, Quickbooks automatically assigns all of the other expense Payroll Items to the same classes, proportionately.  For example, if 10% of your payroll income lines are assigned to one class, 30% to another, and 70% to another, you should find your other payroll expenses on the same cheque being apportioned to each class in the same percentages.

Make sure that Class Tracking is turned on in 'Accounting' preferences.  Also make sure that 'Job Costing for pay cheque expense' is selected in the 'Payroll & Employees' preferences.  

You can test this by doing a report and filtering by Class to see the transactions coming from the pay cheques.  You should see that the CPP Expense, EI Expense, benefits expense and any other expense on the pay cheques are being allocated properly to your different classes.