GTMGMT said:

If I import the time sheets to the paycheck can the system allocate the company EI and CPP expenses as well as any union pension and extended health costs to the projects involved on a percentage of total hours if I set up these expenses to be costed to a GL account that includes all labour costs and additives.

I believe so, yes.

GTMGMT said:

If this were done would it affect some of the existing reports already established in the system?

New transaction entries never touch existing transactional data.  They can affect balances, quantities, etc. but the original transaction remains.  

Pre-existing payroll entries can't be added to by importing timesheets.

New Orders will affect 'on order' quantities, but have no effect on prior Orders or the invoices created from them..

I believe that changing the allocation method (Amount, Percent, Hours) only changes the entry process for the next entry.  Existing entries are what they are.  (but I would test that before changing the Allocation Method!)