oh, man. it's been years since I've done that. from what I remember, you need to use hdd partition fixer to get partition 2 on to the drive. that's the partition that emulates original xbox stuff. then, you have to format it on the system, which iirc requires the serial number of the system. you can get that in system settings. I don't remember too much beyond that, because as I said, it's been years. be careful with opening up the caddie if using a phat, because that spring that holds the eject button can go flying off. good luck finding it if it does. lol
edit: some more info I remember. I think partition fixer is run on the system (not 100%), and I'm pretty sure it won't format the drive in case you already have stuff on it, so don't worry. I can't recall if you have to have a wd drive or not, because that's the way you can get another drive to work officially. I don't think the security (ss.bin) file cares if you have an rgh or jtag, so it probably doesn't matter. anyway, I'm using a 1TB drive in mine, but you can go up to 2TBs internally.