A couple of questions - Have you upgraded to the latest version of the Firmware for Indivision? It adds a few new templates for useful screen modes. You need the Core 2.6 and the 1.5 Config tool. Here is the link:
http://wiki.icomp.de/wiki/Indivision_AGA_MK2Second, have you gone in and tweaked the screen settings for individual screens? You really need to fiddle with the settings for a bit to get each screen to display the way you want.
If you download these two tools and update your Indivision, I can help guide you through setting up the screen modes.
