@TJFBryant, all I can tell you is how mine is set up. I have an existing 8GB card still set up for GP2X. It has the usual folders:
\game
\emus
\ebook
\movies
etc etc.
I created a new \gp2x folder in the root, and dumped all the existing GP2X content into that. (So now the only folder in the root is \gp2x). Then I made a \pandora folder in the root, and set it up as per a regular Pandora SD. I dropped GINGE into \pandora\desktop, and barring any compatibility issues, everything runs fine.
[edit] In short, the trick may be to ensure all GPEs are in their respective subfolders under a 'game' folder.