How do you handle getting a 1099-MISC for a car allowance? Can you deduct the miles you drove in that car for work? If so, is that a "self employment" tax situation?

You need to enter the form 1099-Misc as income on your tax return, in the Other Common Income section, and then Income from form 1099-MISC in TurboTax.

 

You can't deduct employee vehicle expenses on your federal tax return if you are a salary employee under current tax rules. If you are self-employed, you can deduct the expenses if ordinary and necessary for your business. 

 

You can read more about it here:

 

Employee business expenses