Maybe this is not the correct answer but I'll try to explain what I know:
Raw data: You have a file (e.g. "my mempack.mpk") where your savegames are stored (those savegames of games that use controller pack, like "rayman 2", but not "zelda"). In that file, you can store a limited amount of saves, like in a real "controller pack". (You can look at the image). Also you can format this file... It is like a cd image, but it is a mempack image... You can store this file in a directory of your hard drive, and use it with another emulator with nrage's input plugin. And, of course, you can have more than one file, but you can only use one each time.
Not raw data (handled by emulator): You will have those savegames in independent files in your "save" directory. (e.g. "V-RALLY.mpk", "Turok 3; Shadow of O.mpk"), one for each game. These files will be together with your ".eep", ".sra" (saves not stored in the controller pack), etc. files (created no matter what "raw data" option you have chosen). Those .mpk files will be named by the emulator, so they will be different depending on the emulator (it will be more difficult to share it -I don't know if you can rename it, like other save files-).
Edit: Image added.