I no longer have a Kentucky client but when I did, the software defaulted to MFJ because that resulted in less tax.  One spouse had most of the income.  I think if both spouses have about the same amount of income, MFS/Combined is a better choice.  But as I recall there was an easy place to switch back and forth, probably on the state worksheet.  But maybe ProConnect is different now.  I was using ProSeries, then.