Right, lets get this right
1. You can backup you ps3 as many times as you want onto the same external HDD but it is highly reccomended to connect it to your pc and rename the backup to something suitable e.g "EliteMossy v7"
2. To make life much simpler, you should put everything you have on your online ps3 onto your jailbreak ps3 e.g your accounts, map packs etc.
3. If you transfer a patch from your jailbroken ps3 to your online ps3 and then do a restore from an external storage device, everything you done was pointless. e.g you put a custom mw2 patch on jailbroken ps3, data transfer and then restore. you done all that work for nothing!
Hope this helped anyway