The only choices for innings are 6 or 9. I've changed the ERA to reflect calculations for 7 innings, but I need to add an inning for the "position by inning". How do I do that?

You would add a statistic and call it "PosInn7", for example. See the short video which shows how to add a statistic from this link: http://statbook.pachysoft.com/helpvideos.html

After you add the stat, you will need to then add it to the report (video shows this as well).