The only data in the save file that is confirmed to be encrypted is the PKM data; we do suspect the Battle Videos too, but as far as I know no one has actually cracked that structure yet.
Decrypting the PKM data is not hard. It is explained in a straightforward manner right here. The PKM data is located in various places in the save file; boxed Pokémon are located in the "big block" or "storage block", and the rest of the Pokémon (party, Day-Care Center, roaming, etc.) are located in the "small block" or "general block".
The general outline of save blocks are discussed right here, and what we know about loading and / or saving a save file is on that same page.
If you have any specific questions, feel free to post 'em!