I disagree about the "no side comments" suggestion. One of the more interesting aspects of Internet debates I've observed is the way non-participants get to critique and or argue the same questions in a parallel thread. This thread can also be quite useful for the participants themselves as a guage of "how well they're doing". Some debates have improved signficantly when the participants realized they were both getting panned in the Peanut Gallery.
I have seldom seen information or argument presented in a companion thread make its way into the formal debate. OTOH, if info is presented in the companion thread that one or the other participants could realistically use, so what? After all, the thread is open to proponents of either side in the debate.