To answer your first question.. Not at all.. You will simply use this template to "wrap" you site's look and feel (& possibly the existing navigation) around Zen Cart.. No nasty iframes, and it will be seemless.. I'll refrain from flogging you anymore on WHY this won't work.. sounds like you've had a bit of baptism by fire on that score..

cheer up.. it's a "learning fall" as my husband would say..
As for your second question.. I don't see anything obvious.. So it's just a matter of applying the template.. I also sent you a PM..