On opening a note, BS displays on the right hand side a reference pane. At the top of that, one can choose from the references linked to, results from a fast search, and the content of a reference folder. In my case, BS displays here the content of a reference folder I haven't choosen and which I find pretty distracting. For me, the setup in the categories window makes more sense. Or, if you want to keep the structure of the note window, I'd prefer to see no references listed before I hit one of the three buttoms.
You can chose another
You can chose another folder, if the default folder is not the one you want. So when user write in the note, he/she can just drag references to any position in the current note to cite.