The purpose of the “change_id” application, which can be found at the MIOS Download page, is to change the MIOS Device ID, and other settings like to-COM flag, LCD mode and IIC MIDI addresses.
Normaly, the ID field can be specified when you are burning the bootloader into the PIC (see bootloader page). For people who don't own a PIC burner and forgot to specify it when buying a preburned PIC at SmashTV or Mikes shop, change_id can be used as alternative solution - this application reprogramms the ID field.
This ID field is not touched by MIOS itself, and also not by the application. This has the advantage, that you can later update MIOS (if there should ever be a new version) or a application without doing this complicated way to specify the ID again.
This is also the reason, why the device ID is not defined in MIOS - it's defined outside MIOS, because the 1st level bootloader needs to know it as well.
So, just follow the instructions which are described in the README.txt of the change_id application, thereafter you are fine. 1st level bootloader, MIOS and the MIDIbox SID application will find this ID and handle with it.