You can enter the unreimbursed business expenses under Federal Taxes, Deductions and Credits, then select I'll choose what I work on and then Job-Related Expenses under Employment Expenses. You will need to enter ALL business miles driven and vehicle information first in the interview questions. Then as you continue through the interview, it will ask for reimbursement information.
You can potentially write off the mileage driven for work minus the mileage you were reimbursed for. If you are an employee and receive a W-2, you can deduct unreimbursed vehicle expenses as job expenses, but you must be able to itemize your deductions
For instance, the IRS standard mileage rate is $.54/mile. If you drove 100 miles ($54 at the standard IRS rate) but the company only reimbursed you $38.00, you could deduct the additional $16 as an unreimbursed business expense. Even then, only the amount above 2% of your adjusted gross income is deductible.
Note: You cannot deduct the miles you commute to and from work, or any expenses you were reimbursed.