It doesn't matter if you file jointly or separately.
For your house, it seems you qualify for the $250,000 exclusion.
For his house, he qualifies for a $250,000 exclusion, but there is no way to claim a $500,000 joint exclusion. Even though marriage imparts ownership (you technically "own" his home for as long as he has owned it), marriage does not impart residency, and you have not lived there 2 years.
You can claim up to $250,000 on the sale of your home and he can claim up to $250,000 on the sale of his home. You can do this on a joint tax return even though it is two different homes.
