Many things can be done from the "Show all bookmarks" window. But they can be very misleading.
(The following may not be very relevant nor clearly stated. Sorry if I can't convey my point.)
For instance, when you want to delete all bookmarks associated to one tag, it's not just going into the Tags menu and deleting the corresponding tag: this would only remove the given tag from the bookmarks but leave the bookmarks bookmarked (which is the right thing to do when I think of it). Instead, the only way I found is to search from "Search Bookmarks" for the bookmark name and delete from the resulting list (making sure I don't delete a bookmark that just happens to share the tag name in other fields. Sorting by tags may help a bit.)
For complex things, I once had to open bookmarks with sqlite and edit them by hand. Scary experience even though I made backups. (How would it deal with Weave, at the time, was my main concern.)