In the upcoming version I added the ability to download only selected bookmarks to the repository from the browser. Now storing bookmarks in the Keepmark will make more sense, because you will not have to constantly remove bookmarks not related to the current repository.
Now, in the bookmarks settings you can find a list of filters for folders in the browser. If list of filters is empty, all bookmarks will be downloaded. When adding a new filter, you need to specify the name of the folder (or its fragment) from which you want to download the bookmarks.
In the window for the first time I added additional context help, which allows you to see which data from the browser are used to filter bookmarks.