You should file as Married Filing Jointly for your Alabama Resident state return, since you are both Alabama residents.
Alabama will tax all of your income (no matter where it was earned), but give you a credit for any tax you paid to Mississippi.
If this is shown on your W-2, TurboTax will pick that up when you enter your W-2, and you will see a screen in the Alabama State interview about 'taxes paid to another state'.
If the amount is not filled in for you already, you can enter the tax you paid to MS there.
Here's steps for How to File a Non-Resident State Return for Mississippi. You can file jointly there, too. In the state interview, you will be able to indicate what amount of your total Federal income was earned in MS as a Non-Resident.
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