If you are reimbursing employees for fuel used set up a simple miscellaneous deduction like shown in this screen shot in the Company setup:



Then on pay day after entering in the payroll hours and such and clicking the Pay button to calculate the taxes, enter the reimbursement amount as a negative number as shown below in that "Deduction" and press enter. That negative figure will add the amount to the Net pay. Then click Save and Close. DO NOT click the Pay button a second time as it will erase what you just did.