How do I prepare a joint federal return and separate state returns? My husband is active duty military, so his home of record is currently different than mine.

You can choose your active military spouse's home of record as your resident state on your tax forms and file joint federal and IN resident state returns and a VA nonresident return for a refund.  You may owe some IN tax since none was withheld, but you will get a refund of all the VA taxes withheld to mitigate.

In the "My Info" section be sure your military spouse has answered all the military questions. For both of you:  Indicate you lived in IN on 31 Dec and "No" you did not live in any other states. Continue.

Still in the "My Info" section scroll down to the "Other State Income" section and answer "Yes" you made money in another state and select VA from the dropdown list. This will generate a VA nonresident return. Continue.

Enter your income and deductions as normal in the federal interview sections.

Then work the VA nonresident return.  Be sure to exclude all military income and your employee W2 income from VA taxation under the Military Spouse Relief Act.  This should result in a refund of all the VA withheld taxes.

Now you can work the IN resident return. IN is going to tax your VA income as an IN resident which will increase your tax liability there but again VA will be refunding the taxes paid to them.   

Remember to work with your employer to file the correct forms to get IN taxes withheld going forward.