Yeah...that can get messy. And states differ as to how it needs to be done when the two spouses are residents of different states..and that happens a lot for military couples.
I only know NC for this situation, (not GA).
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For NC, NC gives you the choice of filing both MFJ-Federal and MFJ-NC (where the non-resident spouse's income will be removed), or MFJ-Federal and MFS-NC...where the MFS-NC tax return will have to be mail-filed
1) For MFJ-Federal&NC: You would fill in all of the Federal part, indicating one of you as a NC resident in the Personal Info section, and the other as a GA resident. Then Fill in ALL of every scrap of all your income and deductions as a couple. Only when you are entirely done with all those entries (Sometime in February or March 2019), you would start in on the NC tax return. The NC tax return should detect that you are a mixed residency couple, and should switch to what is essentially an NC nonresident tax return (it did last year....2018 isn't up yet). When that happens, and you go thru the interview, First it will show you the W-2 forms that were entered in the Federal section....and you can mark your own as NC Income...and your spouse's ans Not-NC income. That removes hers W-2 income from consideration . Then on the pages that follow, the software presents the Federal amounts for various income types (Interest, Dividends Cap gains, etc)...and you are supposed to indicate what sub-part is to be considered NC income...like maybe half the Interest is yours and NC-taxable.....but a lot for these other ares depends on whether you have joint accounts, or perhaps have some separate band and investment accounts....
When you get thru all of them, and error check everything. You should print them out to make sure all looks right and NC is taxing you only on your portion of the income for the year. I don't know what the NC forms will look like yet this year, but last year on the D-400, they would put your full combined MFJ income in all the way down to line 12, then box 13 is a decimal multiplier which chops down your combined taxable income to a you-only $$ value on line 14...then applies the NC tax to that lower you-only amount. Then you can e-file both the MFJ-Federal and MFJ-NC tax returns together...once you figure out what needs to be done for GA.
2) Or you can file MFJ-Federal and MFS-NC. But to do the split filing for MFS-NC, you would have to prepare a MFJ-Federal tax return that you could e-file by itself.......and then entirely separate MFS-Federal+MFS-NC tax return. The MFS-NC tax return would then have to be printed and mail-filed by yourself, with a copy of the MFS-Federal tax return attached. (the MFS-Federal is not filed with the Feds...just sent in along with the MFS-NC tax return to the state).
Doing any of the MFS situations requires multiple tax files and multiple accounts if you decide to use the Online software...so don't...stick to the Desktop software that allows multiple tax fails to be prepared.
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Next question...is what does GA require for split-residency couple tax filings...I'll prompt a GA expert.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
