All the PocketSNES data should go in the same place TOGETHER, preferably in a subfolder. For the .app version, try making a 3D Game folder within the main GAME folder, then make a "PocketSNES" subfolder within that to keep all the related data organized. For the .sim version, just right in the main GAME folder works fine, or a subfolder. You can make as many subfolders as you want for emulators and their respective data, doesn't matter as long as everything including the games are within the main GAME folder.
As a note though, some emulators, such as VICE (Commodore 64 emu), work alot better if they have the games within THAT emulator's folder. May sound confusing, but trust me, it works. Just think of it as working the same way a P.C. emulator would work, the closer the games are for the emu, the easier it will be for the program (and you) to find and open. This is all for Native OS by the way...
Oh wait, i just caught what you were trying to ask. Yeah, you access PocketSNES.app throught the 3D GAME, on the dingoo's main menu.