Thanks. It helped to know that a) it's there somewhere and b) the word "Miscellaneous" and "your state" are word that can lead you to the field that controls state filing status.

I found it under "General" / "Misc Info/Direct Deposit" - where there's a tab along the top for the State (in my case "IA"). 

There were a long list of items for Iowa there, including a "Filing Status" field allowing a choice between MFJ and MFSC (married filing separate on a combined return).. This was the choice I was looking for. It looks like the software automatically chose the best - MFSC - but in the past I've found it important to check which filing method works best in Iowa.