Root of your flash card is the same level as the r4 _system_ directory.
x:\ (where X is flash card drive letter).
Basically just drag and drop the cbds folder onto your drive letter from windows explorer. this will copy the files to the root of your flash card.

As for chaps asking for themes the comic book ds site is still up and is hosting 3 themes.
None of them tickled my fancy so I made myself a basic uncluttered black theme.

http://cbds.free.fr/Softwares/Themes/