i havent used your distro, ive stuck to suse and slackware but the knowledge should be applicable.
depending on your lilo setup, lilo should be loaded from the superblock (this is like the MBR but for the one partition?) of the the partition you loaded linux on (/dev/hda3, for example). from my hands-on experience, a computer looks for a boot device on a hard drive in the following order: master boot record, first partition superblock, second partition superblock, 3rd etc. if you have windows 2000 installed it attempts to write over the MBR with what i believe is called NTLOADER. this may not be the exact program name but it allows u select OSes to load that are in the win2k's win.ini file. so therefore, you should be booting your system by the ntloader in the mbr before it looks for lilo in the superblocks of your partitions.
in order to boot your linux system you either need a lilo boot disk (what i suspect youre using) or tell ntloader to load your system from a superblock (point it to lilo). if you havent installed win2k than you should still have a clean MBR (unless you installed LILO there). then your computer will bypass the MBR and load from a superblock (the general lilo installation type). if youre getting a lilo prompt then u either erased your MBR (rendering win2k unbootable, but we can fix this later), or havent installed win2k yet.
remember, win2k uses ntloader stored in the MBR to load itself, win9x uses a mechanism stored in the superblock, and linux uses lilo stored in either. to have both win2k (which needs the MBR), and lilo which needs a superblock in your case, you must tell the ntloader (in the MBR) to look in a superblock. this can be done by a program called
bootpart. i suggest a very good howto available at
tweak3d.net.
i use the term superblock to refer to the boot location in a partition. this may in inaccurate but i do mean the boot area of a partition. superblock may in fact be the same thing as an MBR, im not to certain on some of my partition terminology.