1099-MISC Question

What do you mean his boss gave him a 1040?

Anyway, the simple answer is, he just needs to offset the 1099 with the mileage used for business or the actual expenses used...depending on which way he has it set up.

Net effect should be zero, unless he excess expenses against the income or the other way around, he pockets the money paid and doesnt use it for expenses(then he owes the taxes on it).