check out www.fiberglassforums.com for your answer to any fiberglassing question. I ripped all the vinyl off mine but I have seen many go over top of the vinyl. Personal preference I guess but I think its best to pull that vinyl off.
never put bondo straight over the vinyl it wont stick at all. u can glass over the vinyl but make sure to clean it extremley good to get all the armorall and junk off of it. for best results take the vinyl off..