you need to mount the filesystem from the hard-disk to the appropriate places, so that you can run /sbin/lilo
After booting from a floppy, the procedure is something like:
mount /dev/hda1 /new_root/boot
mount /dev/hda2 /new_root/
then you should now be in a root directory (which is actually your two hard disk partitions mounted at /new_root on the filesystem that you have booted to on floppy) and from there can run /sbin/lilo
This is assuming that your "/boot" partition is /dev/hda1 and your "/" partition is /dev/hda2 you'll have to make the appropriate substitutions.
Good luck, its been a while since I had to do this, so don't quote me on any of the above