I'll try that thank you...
Ok so Minecraft came as a PKG game. I installed it through the REBUG PKG installer. When the game launches it says "Minecraft PS3 Edition" has failed to load, and cannot continue.
Ratchet and Clank came as a set of folders. I copied the folders over to the PS3. I then selected the folder and chose to Copy-to-ISO into the internal PS3ISO folder. I did as suggested above and did the webman refresh and then it showed up under the webman folders. Just as when I launched it with multiman though, the game gets to a screen that says it needs to install game data onto the internal HDD and I need to push X. Then it seems like it is frozen because I push X and it does nothing... nothing at all.
**Went back to the books**
After some more research I have solved my problems. Thank you to everyone that stopped by but was not ready to reply yet.
As for Minecraft, the PKG I had was bad another one from a different source fixed the issue.
As for Ratchet and Clank, I am going to assume there was a quirk in the system when I transfered the Folder/Files over to the PS3 and then tried the Copy-to-ISO method. The reason I make that assumption is based on knew knowledge. I found a PC app that handles verifying Folder/ISO games that also converts Folder games into ISO (PS3-ISO-Rebuilder). When I verified the Ratchet and Clank Folder game everything was fine. I used the same app to build a new ISO and transferred it over to the PS3 and the game worked no prob.
Ok so all that being said... I now have the knowledge to answer my first question....
ISO Game - Use an NTFS drive, Use IRISMan to transfer the ISO to the PS3
Folder Game - Use PS3-ISO-Rebuilder to convert to ISO and then follow the above
PKG Game - Use the Package installer built into REBUG CFW/IRISMan