definitely would suggest the desktop software. Iowa allows you to file as married filing separate on a combined return or married filing separate on separate returns. you can also check the married filing jointly option. then you can choose whichever option you wish.
use labels such as the following to save the files before e-filing
1.federal and joint iowa
2. federal and combined iowa
3. federal and MFS Spouse 1 Iowa
4. MFS Spouse 2 Iowa
delete the ones your not going to use to leave the following
1. or 2. or 3 and 4
https://tax.iowa.gov/expanded-instructions/filing-status-2020