I have two 32GB cards in mine. In the left slot, I have folders "A" through "M", and in the right slot I have folders "N" to "Z". Each folder (except the "Pandora" folder) is a single letter. For example, SNES ROMs are in "A", Megadrive are in "B", Speccy in "C", Amiga in "D"... you get the idea.
That way I can not only quickly locate what I'm looking for (Oh, you need a copy of Turrican for GB? That's in folder "J" then!), but I know which SD Card a particular game or PND is going to go onto - Emulators that use ROMs in the first 13 folders sit on SD card 1, others on SD Card 2. If one SD Card gets full (I used to have a 16GB card in the left hand slot, and PSX ISOs would fill up the "F" folder) then optional numbered folders can be used on the other SD Card - "1" would be for overflow Spectrum games, "2" would be PSX, "3" would be GBA, "4" for GB etc.
It's a neat way to do things, and keeps the ls listings tidy!
D.