Well if you can get some games to work your doing it right. i don't believe the PS3 can tell the difference between a downloaded game and a game you personally dumped.
i have not tried this rogero manager you mentioned but it must work if you can play your original games.
can you tell us what game it was that you kept trying?
what they mean by patch can be either of these things depending on the manager you use
1. patching the param.sfo of a game that requires 3.50 firmware to work on 3.41 (Medal of Honor for example)
2. patching used to make games with controller issues work correctly (this is only needed to play F1 2010 believe)
make sure you check the Game Compatibility list to see if a game you download works or not.
how did you transfer the games to your ps3?maybe the FTP client you used didn't transfer the game correctly and that is why they dont work. i think most people use Filezilla for PC (I use Cyberduck for Mac)