I'm at the itemized deductions screen, I'm filing as married, but separately, we don't know what any of that means. She already filed her taxes. Do I need to check box?

Did she claim mortgage interest, charitable deductions, and state and local taxes as deductions on her tax return?  If she did, you must select yes to that question and also itemize your deductions.  If not, then you may claim the standard deduction of $12000.