Yes you still file a Joint return as normal. Joint still should be the best way. You will just add Schedule C for your business. Or what kind of business entity is it? Are you a Single Member LLC? If you are not a SMLLC filing as a S Corp it is a disregarded entity on Schedule C.
It doesn't matter on your tax return if you have an EIN. You give your EIN to people who pay you so you don’t need to give out your ssn. Thats if they need to give you a 1099NEC to report what they pay you.
