Lilo can be installed into the Master Boot Record (MBR) or as the first part of some other disk partition. That is, you have the choice of the BIOS starting up lilo or some other program in your MBR. The MBR program that cames with Debian is installed when you run the command install-mbr. To overwrite the part of lilo that is installed on the MBR you simply install something else in the MBR!
When lilo overwrites the MBR it keeps a copy of the old MBR in case you find you need to restore it for any reason.