Scrolling/selecting in a long bookmark folder list is tedious for moving multiple bookmarks to the same new folder.
Consider saving/displaying last destination folder when moving bookmarks. Also consider adding "Copy Bookmark".

The design is set up so that you create a folder, then you select that folder, and collect all your bookmarks to that folder. For example, before a sermon, I set up a folder for it. Then I just collect bookmarks throughout the sermon. It's quick, because I don't have to select which folder things go in -- I can concentrate on the sermon and just collect the bookmarks for later.

The downside, of course, is what you've described -- it's not easy to move the bookmarks around. Our upcoming desktop version of Mantis will make that much easier, though. It's due later this summer.