I won't specify wich xbox you'll do all this, since I got a bit lost while reading your post, but here's the proccess to flash your virgin EEPROM into whatever xbox you want to flash it to:
FTP Configmagic FINAL to your xbox APPS directory.
Within Configmagic folder, there's a folder named "DATA" and inside that folder, you'll put your "EEPROM.BIN" file. Overwrite any eeprom.bin file in there with yours.
All you have to do after that, is go in configmagic, hit START, and then "Load EEPROM.BIN from file".
THen go to the menu again, and select the option "Update XBOX EEPROM".
That's it. your EEPROM is flashed to your TSOP.
EDIT:
PS: If you do this to a softmodded xbox, consider doing a split TSOP flash. Check the tutorial section for info on how to do it.
And like Sidewinder said, your eeprom has to be compatible with your xbox version.