Your employer is not treating you as an employee if they gave you a 1099 (as opposed to a W2). This complicates the matter, as the Military Spouse Residency Relief Act doesn't cover self-employment income. If you got a 1099-MISC, you are treated as having a business in Maryland. You would need to file a nonresident Maryland return.
If you elected military spouse tax treatment, and you were treated as an employee, you would have had no state tax withheld. You would be treated as a resident of Florida, which has no individual income tax on wages. No state return would need to be filed.
The primary thing you need to do before you can move forward is to decide whether you want to dispute being treated as a nonemployee. Because, as an employee, you would not have to pay state taxes if Florida is the proper military domicile.
If you think you really were a contractor, choose Maryland as Other State Income under the Personal Info tab and allocate this 1099 income to Maryland.
