Like you, I'm not sure that I like the changes in Bookmarks that they made in FF 3.
You have: Some folders / Stand alones / Rest of Folders. All are sorted.
1. I'm not clear if you do or do-not want them sorted.
--- If not: Organize Bookmarks > Views > Sort > Unsorted.
2. Are you able to move (drag and drop) the folders in the second section into position to follow the first set - or wherever you want them? I can do this in the sidebar. I haven't worked enough with Organize Bookmarks to understand the interactions / viewing differences between it and the sidebar.
You do know that Bookmarks now are in a database, not in an html file?
Down at the bottom of the sidebar is a section 'Unsorted Bookmarks'; mine is empty, and I don't know if
I am supposed to put things there - for later repositioning - or if this is for FF's use. I just ignore it.
UserAgent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.0.1) Gecko/2008070208 Firefox/3.0.1