I put a folder CALLED GAMEZ all caps in the root of the drive (when you open the drive) Put your games in there Best advice is if they are named like Dantes Inferno for example then inside that folder there is another called BLUS30405 Move or Cut/Paste the BLUS30405 Folder into the Gamez folder and delete any folders with the game names.
This was what drove me crazy for 3 days (giving a eboot.bin error). Hook the ext drive up to the JB PS3 Open your BackUp Manager I prefer Open Manager 1.142. Then Copy to Int HDD, then hook up your friends HDD and copy them to it. If you are only using a PC then that folder setup is all you have to do. I copy mine to ext. hdd and then hook it to PS3 cause the ftp is way slower than the ext. hdd to transfer.
My Ext HDD is a WD320GB-SATA hooked to a usb adapter with a power adapter since its a full size drive. I also have a Hitachi 40GB SATA Notebook drive that is hooked to a seagate freeagent go dock and it works fine also. Acronis is a great app I use it all the time.
If any of this doesnt work try Formatting the HDD from the Disk Management in windows selecting FAT32 and "Default" for the Cluster Size and choose whatever name you want.