Capturing complex shop floor wages to reflect actual cost

We have a complex unionized shop floor and looking to make time recording easier for the lead hands. Some employees may work three different jobs at three different pays in one shift. Shift differentials, first aid differentials, meals and clothing allowances, etc…Willing to look at other programs that can be linked with Epicor. Does anybody else have this issue? A good work around? Capturing an average cost using overhead rates can work but not enough detail for payroll.