as an employee, that car allowance is supposed to be reported on your w-2. it seems your company does not have an accountable plan just gives you a flat amount periodically. under an accountable plan, you would only be reimbursed for the business mileage at no more than the IRS standard mileage rate and need to submit reports to the company about usage. under an accountable plan, there would be no tax reporting for you unless you failed to submit reports.
you can go back to your employer to get this corrected. if it won't then you have a reporting problem.
you could use Schedule C, which is improper. if you did, no vehicle expenses would be allowed even for
business use because tax law changes have eliminated the ability for employees to deduct job-related expenses. you'll end up paying medicare, FICA and income taxes on the allowance.
your employer also faces tax issues in misreporting employee income. and failure to withhold and pay the payroll taxes.