Contractor rates can be set up in the system for users who get paid differently than what they bill at. For example, if a user bills a client at $100.00 an hour but they get paid at $75.00, the $75.00 would be their Contractor Rate. You can then run the Contractor Summary report to see the amount billed and the amount they should be paid.
Set up their rates in their User Profile:
Contractor Summary Report: