I know how to do Utah. Apportionment (using the combined factors of the 1120S and the 1065) is done in what Lacerte called Screen 50.131. In ProConnect, it would be under State & Local, Apportionment, Utah. Withholding goes in Schedule K, Passthrough K-1s (same place you'd normally do the K-1 input), Utah Credits and Withholding (way down at the very bottom), under TC-250. You'll have to pick the type of withholding you have from the drop-down.

You need to have an Excel file to tell you what you expect the right presentation and the right answer to be, and then override judiciously until you get there. It's possible there will be one or more states that can't be gotten close enough to e-file, and you'll need to swap out pages to create an accurate paper return.