Just a few pointers:

It's generally best to put Lilo on the mbr of the first hard drive (hda). Really, the only chances of corruption are of Windows overwriting the mbr. Lilo cannot boot from the second mbr unless you switch your bios to boot from that drive (an option not available on all bioses).

For a boot floppy to work it generally needs to be fully formatted (rather than a quick format).

An alternative would be to switch drives (so that Linux is on hda) and use Grub (apt-get install will find it). Grub can convince Windoze that it is on the first hard drive. Consequently, you have a boot loader which Windoze cannot destroy, and no floppy to loose. You can -- indeed, should -- write Grub to a boot floppy until you're absolutely happy that it works.

Grub's syntax is pretty free form and I'm currently using Lilo, but a search for Grub here (or boot floppy) should find something and, of course, there are the HOWTO's.

/usr/share/doc/HOWTO/en-html/mini/Multiboot-with-GRUB
/usr/share/doc/HOWTO/en-html/mini/Multiboot-with-LILO
/usr/share/doc/HOWTO/en-html/mini/LILO
/usr/share/doc/HOWTO/en-html/mini/Linux+Win95
/usr/share/doc/HOWTO/en-html/mini/Linux+WinNT

Hope that helps a little: it's not meant to read as RTFM!