When you work through the Georgia return you need to indicate that you are a non-resident of the state. You will see a screen for all your categories of income on which you can indicate the amounts that belong to your resident state:


You can see on the tax summary that the income applicable to Georgia is subtracted from the Gross federal Income:

When you do your Alabama tax return, you will include all of your income, including the income earned in Georgia, and you will get a credit for taxes paid to Georgia, so you won't be getting double taxed:

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