Are you a military member?  What are "SO's" orders?  Reply to this post for help with your question.

We aren't military. He's a diplomat from Brazil and posted to NY until summer of 2021 unless we extend.  

We have something like the equivalent of a common law marriage in Brazil. 

NY law says that you were a resident due to your time in NY. You need to file NY resident return. VA qualifies you as a non-resident.

Your resident state taxes all income but gives a credit for income taxed by another state.  Please carefully follow these directions.

You will need to prepare both NY and VA in a special order. You may need to delete both states and begin again.

1. First, prepare your non-resident VA return. This creates your tax liability for the non-resident state. See How do I file a nonresident state return?
2. THEN prepare your resident state NY return and it will generate a credit for your income already being taxed in the non-resident state.
3. The credit will be the lower of the state tax liabilities on the same income. You may owe your resident state.

It isn't possible for the program to create a credit before it knows the liability. Your returns may be wrong if you do not prepare the states in this order.

Virginia actually qualifies me as a resident as well because my permanent address is there, my drivers license is there, my voting registration is there and I intend to return there if we are ever in the US without my SOs orders. 

Would the process still be the same?