Well, damn. So I started recording a video to try to explain the issue I was having better, and it seems like I may have figured it out.
https://www.youtube.com/watch?v=2fO4z18HBy0&list=UUf87dyQP0Q50Tmy-H7zqqIQIt looks like when the Amiga is using the PII to display an image, the Indivision is still outputing some kind of signal. So that's why my screen when black when I plugged in the pass-through - it was trying to display whatever minimal signal the Indi was sending.
I found one thread that mentions this sort of, here:
http://www.amiga.org/forums/showthread.php?t=65148Possible solutions:
- find some sort of software to completely disable Indi output when the PII is on. Maybe a setting in P96, or something in CGX (as mentioned in the above thread). Don't really want to switch to CGX now that I've got P96 working...
- find a video card that ignores this non-signal the Indi is sending out (possibly @matt3k's GVP Spectrum?)
Any other ideas? I'm getting there, I think, sorry for the long rambling video, LOL.

Edit - On second thought, I don't think that is the case, because then when I have an Amiga screenmode displaying through the Indi, if I plug it into the PII it should pass it though. Gaah, this is getting way more complicated than it needs to be.
