When you start your federal return, when entering the information under the Personal Info tab you will be asked the resident state question and the AD MIL question for each tax filer separately. Just select accordingly. It is VITALLY IMPORTANT that both of you claim your individual incomes for your specific state of residency, and that you properly indicate what income belongs to which tax filer. If you do that, then it will be easier on your state tax returns to exclude the income of the non-resident spouse.
Also, most states exempt military income from state taxes if you are stationed by PCS orders outside the state and earn that income while physically outside the state.
If tax filer A is "NOT" stationed in their home state, and tax filer B has non-military income in that state, MSRRA applies (sort of) to that non-military income under another program. I'll go into detail only if necessary. But I would need to know the HOR of each tax filer and the state where you are both currently stationed.