You have what is called a non-accountable plan. Your employer gives you an expense allowance and does not require you to substantiate it with receipts or pay back any excess if they pay you more than your expenses. Under a non-accountable plan, the reimbursement or per diem must be included on your W-2 as taxable wages and subject to income tax, social security and medicare taxes. Then, because you are paying your expenses with taxable wages, you are allowed to deduct them subject to the usual rules for work-related expenses.
If this is for work use of a personal vehicle and you are a W-2 employee then you can deduct your expenses as an itemized deduction subject to the 2% rule using form 2106. These limits mean you will get a reduced or maybe no deduction depending on your other tax facts. You can deduct work-related mileage using the standard mileage rate method or the actual expense method. The standard rate is easier and usually more lucrative. You need a diary or log of your work-related travel with the date, business purpose, and mileage driven. The mileage rate includes allowances for fuel, repairs, insurance and wear and tear so the only thing extra you can deduct is tolls and parking. You can't deduct your daily commute but you can deduct other work-related trips you make according to the rules in chapter 4 of publication 463.
https://www.irs.gov/forms-pubs/publication-463
