So I've slept since I did this a couple weeks back so ignore my last response. I went back and tried again and remember things again. I go through the seasonal income for Indiana just fine.
The problem, as stated in my original question, is that the state withholding for the year are divided by 4 and split across all 4 quarters when they were actually only paid in the first 2 quarters. The federal asks is you want to apply withholdings evenly across all quarters and the state does not. In our case all withholding were done in first 2 quarters and if they are applied correctly to the first 2 quarters then there is no penalty when I do a 2210A by hand.
So, if TT would let the withholdings be applied as paid, like it does for Federal, then this would not be an issue.
