My husband works as a uber driver. Is it best I still file jointly? I think he would end up owing the IRS and they would deduct that from my taxes. How would this work?

[Critter]

It is better to file a joint return most of the time  so start thinking OUR tax return and OUR refund or balance due and not HIS taxes owed coming from MY refund.  What HE needs to do is pay in quarterly estimated taxes ... OR... YOU need to have less withheld and keep YOUR money in your pocket during the year. 

If you really want to keep MINE & HIS separate then go ahead and file separately  but be aware it may cost you more in the long run that way. Compute the returns both ways to see the differences before either of you file.