Is your xbox chipped or modded?
For softmod, you will need your eeprom backup to lock the hdd again (with a PC) before putting it back.
For chipped, you can unlock the hdd.
Once unlocked, any 1:1 disk imaging program will do a backup of your xbox hdd. I use SelfImage.
Softmod will need to lock the hdd again with xboxhdm before you put it back into the console.