If this allowance was from your employer, it should have been included on your W-2, because you didn't have to account for it. Are you sure that it's not included as part of your wages?
If it's not, you should use the amount of your allowance to reduce the amount of your automobile expenses claimed as a miscellaneous job expense. You will reach a screen asking if you received any reimbursement for your expenses (see the screenshot below)
If your actual expenses are less then your reimbursement, you would actually have additional income that will be added to your return.
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