this is what I did to softmod my xbox.
1: take out the origional xbox HD and use hd_driver to back it up (using the hotswap method). this will insure that if you screw anything up, you have the origional vergin state of the box so you can always use hd_driver to restore it.
2: once backed up, use what ever method you want to mod it. I used the origional HD and xbxhdm and softmoded it that way following
this tutorial.
3: once modded, used evox to create the the backup of the eeprom and hd key. ftp this over to the PC and put it some where for save keeping. also, it wouldnt hurt to copy over the C: and E: partitions by ftp (so you can use your save games and the modded files later.
4: now, take out the origional HD and re-load the vergin iso back onto the origional HD, so you can put it away and use it again for what ever reason.
5: using the files that you copied from step 3: use xbxhdm to install the mod onto the larger HD. xbxhdm has the option so you can include files that you want to be copied over in addition to the hack, so this step will automaticly copy over your game saves and hacked files from C:
I know that this is a time consuming process, but this is how I installed a larger HD into my softmodded xbox. if someone has an easier way, by all means post it!