To report restitution, you’ll want to utilize the multiple paychecks option under Paycheck- Deductions, Payments, and Notes towards the bottom of the payroll record on the week the work was done:

And be sure to mark the second check as Restitution:

Then simply make adjustments to your Gross Employee Pay This Project, Hourly Rates of Pay, and possibly Fringes to reflect what was paid after all was said and done: