I do agree that the mgmt is not that intuitive, especially if you are using List mode. But what you can do is to Click & drag, as if it was your Desktop. I've attached a print screen, hope it helps to understand. What I usually do to ease the process, is to change the view mode, to the option in the middle, on the top left corner.
I'll look at that again but I've done many bookmarks that took a little finesse and I do always check every folder before I consider I have a problem. But I make mistakes like all so I'll check that again. However if 2 folders I found under one folder, tree whatever you'd call it were 2 of my bookmark headings seems all should have been there? But I usually always check IMPORTED. I'll get back to you if I have overlooked that for some reason and hearty THANKS! for taking time to answer. Jack ":-Dx