Hi Saulo,
Saving bookmarks in the database (done by right-clicking in the bookmarks panel and selecting "Dataset>store in dataset") was a bit of an afterthought and a quick and dirty hack. But, I've given a shot at fixing the issues you brought up.
I added the ability to delete sets of bookmarks from the DB by right clicking in the bookmarks panel. I also changed the behavior of the store operation so that you won't get duplicates. It now confirms then overwrites any existing bookmarks.
There's still one small gotcha. The program identifies a set of bookmarks by the name you give it (that appears at the top of the tab). So be careful to use a unique name when you intend to create a distinct set of bookmarks. I also added a "rename" item to that same right-click menu, for this reason.
The changes are deployed now in version 0.9.161.
I hope this helps. Please let me know, either way. Thanks!
- Chris