To apply using both incomes, you need to both be on the loan, and therefore, both your credit and his credit will be used. It doesn't matter if you file your taxes married filing jointly or separately.
The good thing is that auto lenders are not like mortgage lenders. There are several auto lenders that will use the best score of the two applicants, as opposed to mortgage lending where they always take the lowest mid score of the two applicants.
Starting Score: ~500 (12/01/2008)