I hit this prob too. I could never get the game (well WB at least) to make use of an entirely new side (e.g. the Boss general). Im sure theres an internal listing that it sticks to. For some reason, adding a new side does not automatically qualify it as an available SkirmishSide and thus you cant script for it in WB. The only viable alternative is to modify (replace) an existing one.
Unless of course RV knows better
Saying all that, when I first hit the 'side list is screwed when you import SkirmishScripts.scb into ZH WorldBuilder' issue, I took a detailed look at the file and Im damn sure I saw a folder for the Boss general in there...