I organize in sets of 10 my own patches by category:
00X are scratch and init templates (bass, pad)
01X are basses
02X are leads
03X are keys
04X are patches playable like keys
05X are pads
That way if I want, say, a lead I can key in 020 and quickly scan through a few options! It works for me because I focus on getting a few presets I really love rather than making new ones all the time.
Everything else is for messing around, factory, and patches I've bought. Eventually I'll probably clear out the 100s once I need more room for more of my own patches as well, keeping the same groupings (12X would be for more leads).