Hi, the Pub 3 does not give specifics in "how to" get the Military Spouse Relief works in every state. 

What I do, is whatever State is in the Service Member "soldier" W2 Box 15 is the Home of Record.  If it is convenient for the Spouse to pay taxes to the Service Member's State then I applied the Military Spouse Relief.  That is adopting the Service Member's Home of Record as own. That will automatically make her/him NR to the state showed in her/his Box 15.

Every software is different.  Some allows you to exempt the Spouse's income in the Adjustment/Subtraction Section of the States, other's to enter a (-) minus in front of the amount or to check a box Qualified Military Spouse Active Duty like in ProConnect.  

I hope this helps.