Internet forum tradition dictates the quoted post goes at the top, and your reply below it. I don't find it all that confusing, but I've been doing this junk since about 1985.. Also, it's probably only necessary to quote the most recent post, not the entire thread.
I believe what some may find confusing is that often people assume the last reply is in regard to the previous post. If that part that one is remarking on is not quoted many assume it is in regard to the previous post, and if it was not it leaves some wondering what "was that supposed to mean?" If what is being replied to is quoted at the top or bottom it seems to make it easy to follow. I think maybe, but I am often wrong.