The way the software works is to take the total mileage figure and the amount that you were reimbursed and reduce the allowable deduction by the reimbursement amount.
If you don't want to enter the total business mileage and skip entering the reimbursements in that section, you could extrapolate the mileage amount down to the unreimbursed portion by taking the total business mileage and multiplying it by the percent unreimbursed - .40 (or 40%). For example, if you had 10,000 miles you would enter 4,000 miles into TurboTax.
You would need to keep mileage documentation for the next 7 years in case of an examination.