If you file a joint federal return and one spouse is a full-year Illinois resident while the other is a nonresident, you may choose to file "married filing separately." TurboTax will divide each item of income and deduction shown on your joint federal return between the separate Illinois returns.
If you choose to file a joint Illinois return, you must treat both you and your spouse as residents. This is not ideal since you live in Texas, which has no income tax.