If you and your spouse are filing a joint federal return but you work in or are residents of different states, you may need to file separate state returns. Sometimes this is required by state tax law; other times it is to your best interest to not include your non-resident spouse's income on your state return. Otherwise both states may try to tax the same income.
The calculations you need to do can be done in TurboTax online, but it is easier to do them with the desktop software. (If you started online, and want to move to desktop, see the TurboTax FAQ below.) You can file up to 5 returns using the desktop software. It will be tedious, but it is the best way to accurately minimize your taxes.
Please see our TurboTax FAQ below on how to file a Joint Federal return and Separate State returns.