It depends on how you're reimbursed and which method you use for deducting vehicle expenses. The software will walk you through this, as well. 

If you're reimbursed before taxes, then you can't take a deduction for any of the costs you were reimbursed for (but you can take any additional costs). If you're reimbursed and it simply increases your W-2 box 1 wages, which means the reimbursement is taxed, then you can take a deduction for all of the job expenses (they're technically not considered reimbursed). You'd need to look at your pay stubs and W-2s to figure this out.

For the vehicle deduction, there are two methods to calculate it; 1) the standard rate method and 2) the actual expense method. The standard rate method takes all of your business miles, times .54 cents per mile. For the actual expense method, you must keep track of all of your actual expenses (gas, tires, maintenance, everything) and times the total of all vehicle expenses by the business use percentage (= total business miles, divided by total miles driven during the year). This method requires much more record keeping, so the standard mileage method can be easier. If you use the actual method, then you can include your tires and take the business portion as a deduction. 

The software will walk you through these methods for the deduction, under Job Expenses.