In the program, report your total mileage. A couple pages later, there is a question about whether you received any expense reimbursement that was not taxed. Enter your total dollar amount of reimbursement here. Turbotax will subtract it from the mileage amount and take the deduction for whatever is leftover. Don't report your reimbursement if it was included in your taxable income -- if included in your taxable income, you are entitled to the full deduction.