That is a very good point: Get organised before you start out!
I organise my set-up's slightly different: First I have folders for all the keyboard "modes" / "features". So that would be Styles, Audio, Multipad, Midi, Registrations, voices, Playlists, etc. Remember that the Genos (and Tyros) is not the same as a Motif synth - it requires a different type of folder structure.
And after that, yes you would use sub-folders. Here I would weigh the depth of the folder structure vs. how fast you need to access stuff.
Heidrun at Soundwonderland put together a really nice folder structure that I find makes good sense. If you head over to
https://soundwonderland.de/pages/en/service/help/support-for-genos-players.php you will find some very informative tips. There is also a YouTube video that talks about how many USB sticks to use and where to use them, etc.
If you download the .zip file on that page - there are two very helpful documents included. Just make sure the Web page is set to English (top right corner) so you get the right version.
Hope that helps. Cheers, Roland