Why do you think you have to file separately?  When married you can file as Married Filing Jointly even if one spouse has little or no income.

You being self-employed as an independent contractor/sole proprietor is not a reason to file separately.  You enter your income and expenses on a Schedule C which is part of and included with a personal tax return, Form 1040.

My wife earns a full time salary as a math instructor at a community college. I thought businesses should file separate.