Well, its a bit complicated to follow, but what happens is:
The EBOOT.BIN on the disc is encrypted twice. There is the ELF, which is encrypted to the SELF, which is yet encrypted again to put on the disc. This second encryption is on every file in the PS3_GAME/USRDIR path.
The patch and method that is needed on the eboot.bin is as follows. First the original is backed up to a PC, followed by playing the original. While the game is running, we dump the game's memory.
Once the games memory is dumped, we have the fully decrypted EBOOT.BIN, then it needs to be manually reassembled- which is quite a pain. Once that is done, some offsets are patched.
Then it is resigned for a development unit, which is then burnt to a disc, or mastered to a USB HDD.
Any questions, just ask!