I am similar to Craig, At the highest level I have folders called STYLES, REGISTRATIONS, MULTIPADS, VOICES, TEXT and TEMP. There is not one for songs (SMFs or KAR)
With the exception of STYLES all the other folders are at this single highest level.
TEMP includes anything that I am currently trying out or working on at the time and once completed the files are then moved into the appropriate directory. Also in there are a few AUDIO (HD recording) files whilst in progress which get moved ont my PC.
I also split the STYLES folder into the T2 Factory style types.
When I had the Tyros1 I got into a right mess with stuff all over the place so now I also use a USB drive which is where I have all the stuff that is not used for gigging or preparation for gigging.
This is where I keep all the Midis, KARs, converted styles, downloaded registration files etc. and they now only make the HD if I am going to use it or work on it.
My advice - Keep it simple. If I get a request for a song that is not part of my usual set I can find a style that is fairly close reasonably quickly as there are not hundreds to trawl through and by knowing what you have at your fingertips you can more quickly decide which to use and get it selected and started with tap tempo...
Regards - Keith