Congratulations - I saw you hint that you'd gotten it in your offline Wikipedia thread.
I hope you're enjoying it.
Regarding PNDs, you need to create five folders. One, in the root of your SD Card, called
pandora, and four in that one called
desktop (to make PNDs appear on the desktop),
menu (to place them in the menu),
apps (to have them show up in both places), and
appdata (this is the place where applications will put some files - at this time, some emulators may require you to put some things in their uniquely-named folders that will appear in there).
As for the rest of the directory structure, that's mostly up to you - but as noted above, some apps need you to put certain things in appdata.