Thanks PDX -
I did figure out my issues after playing with iReal a bit. Adding spaces to manually get the right number of bars per line seems to be the way to go, and iReal skips any bars that don't have a chord symbol in them. (Slightly odd, but it's fine now that I understand it know what to do!)
The next issue is that I'm trying to create an intro vamp, followed by the head, and solo choruses, but I can't get iReal to repeat back to the head, it seems to repeat back to the top of the form.
Everybody Wants To Rule The World - Tears For Fears
In this chart the first solo chorus seems to go to the right place (first repeat on bar five), but the second solo chorus (last head since i have it only playing three choruses) goes back to the top of the form.