Recommended config: (or at least what worked for me) for least trouble:
-primary hd as only drive on primary ide channel
-xbox hd as only drive on secondary
though I have gotten it to work on my ata100 port before, you might as well try this out
both ide ports support harddrives. it isn't detected for some other reason (I got this before too. follow these steps, and above all, try try again)
what I did with my 2k machine:
-either master or cable select works. I would recommend you leave it on cable select
-leave xbox power cable in harddrive, ide cable in harddrive
-let xbox boot to game menu or something that isn't going to use the harddrive too often
-boot up computer, as soon as possible (right after the vga bios, during memory test), press the Pause Break key, right next to the scroll lock key, above page up.
-after the computer's startup is paused, unplug the xbox hd cable and plug in the one from your computer.
-hit any key to continue
-check and see if the bios detects the harddrive. if it doesn't check all the steps and try again.