the eeprom.bin file is the biggest problem when you softmod. Once your xbox is softmodded, it is easy to run a application to backup the information that is in that little 256 byte memory chip. However, you need that information to perform your softmod as a softmodded xbox harddisk must be locked with the right password. That password is calculated from the eeprom unique hddkey and the harddisk model and serial number.
Before I make this community angry, I should tell that there are other methods to softmod the xbox.
1. Hotswapping. The xbox unlocks it's harddisk. After this has happend, the ide cable of the harddisk is disconnected and the cable from a pc motherboard is connected to the disk. As the disk is unlocked, you can alter stuff on it and install a softmod.
2. Game Exploit. Trough a action replay, a gamesave is installed on the harddisk that causes the game to run unsigned software. You will need a original game that is exploitable.
3. Install a modchip. Once a modchip is installed with the proper bios, you can run the applications to backup the xbox eeprom. Once you have that backup, you can remove the modchip.
4. Build a eeprom reader. It are just a couple of resistors and a couple of zener diodes. They allow to interface your pc serial port with your xbox IIC bus. That way, you can read (and even reprogram) the eeprom chip.http://forums.afterdawn.com/thread_view.cfm/357863
Most people try the hotswap since you don't need any additional hardware and soldering work. It is a dangerous option that can damage your ide port as it wasn't designed to be disconnected with the power on. If it doesn't work (for instance because you added a wrong file to your harddisk), you will end up with a non functional xbox. It is often difficult to revert your work and start over.
I prefer the eeprom reader. It is the cheapest option after the hotswap. You can build a new harddisk from scratch with it, leaving the stock one untouched.
The choice is up to you.