Without any trolling I must say, that I am also pretty confused with the software. There really is a lot of room for user interface improvements.
I completely agree with your every word about too many menu items that all do similar shit - open project, import project from pedal, etc etc. This must have been done easier…
BBManager project is logically structured completely different from how it is physically located on the drive - and that’s my own main concern about it.
First and foremost - you shouldn’t ever look into the BBWorkspace folder. Treat it like that - it is not for you, it is exclusively for BBManager to use. No way in hell you can ever change something there (unless fully prepared) for BBManager to alter its content accordingly. Just completely forget about that folder. It will be easier this way.
Store your own files elsewhere - totally where you want them to be, but not inside BBWorkspace folder.
Second - use BBManager to build a full song from your MIDI patterns (that are stored wherever you wish outside from BBWorkspace). Use Import - Export > Export Project to Pedal to load your modified content (with added/removed songs) to the pedal
Third - get acquainted with the concept of the “content” - they are the four folders DRUMSETS, EFFECTS, SONGS and PARAMS. They are located somewhere inside BBWorkspace, and you can manually copy them to the root of the SD card if you are having issues with Exporting Project to Pedal.