I have 4 onboard sata drives, I was curious if i could just plug the hitachi 47d into sata2, and turn the 360 on and run xtreme.bat from there? Will that work?
No this will not work. You're Hitachi has to be set to a special debug-mode (referred to as ModeB) to be recognized by the Windows OS. In the standard mode the drive won't response to the standard "Inquiry" command and therefore Windows doesn't recognize the device.
My suggestion: Search for one of the tutorials geebee made, it probably has all the answers you're looking for.