Perhaps a look in the emulator section may yield results?
I have a soft modded wii and I have a 1GB SD card with homebrew, many emulators for various systems, Diomios, Sega, Nintendo, Nintendo 64....etc My problem is I have a 1TB hard drive partitioned about 5 different ways. I have one section for ROMS/Games n such for the emulators. I can not get any of the emulators to "pull" from the USB. I have the section with the games partitioned FAT and I have tried FAT32. I also have this partition set to primary and backed all other partitions off to logical. still no dice. The WiiSX wont find any of my PS1 games on this partition. nor will Wii64 or any of them really.
Most apps won't know how to locate any partition other than the first. You may want to consider reformatting the drive so it is one larger partition and placing the files in separate directories on that drive.
In terms of the emulators, each emulator is expecting the ROMs to be in specific places anyway, so having them on a completely different partition will make them impossible to find.