On the assumption that Win2000 boot load is still like NT (90% sure it is) you need to do the following.
Check where you have lilo installed to on the second drive (boot record/super block). Now you need to get a copy of you boot block to give to the Windows boot loader. To do this use dd to extract the first 512 bytes of the superblock/boot record:
(assuming that LILO is installed on the superblock of your first linux partition on your second IDE hdd)
dd if=/dev/hdb1 of=bootsect.lns bs=512 count=1
Now that you have your bootsector copy this to you c:\ and edit boot.ini - you will need to take off the hidden & system attributes, so:
attrib -r -s boot.ini
now edit boot.ini to add the following under the [Operating Systems] section
C:\BOOTSECT.LNX="Linux"
not put reset for attribs
attrib +r +s boot.ini
Now reboot and hopefully you will see an option in your menu called 'Linux'
You will need to repeat the process whenever you update your kernel/lilo settings - please remember to do this or you'll be back to you boot disk!!
Check out the following for more details:
http://linuxdocs.org/HOWTOs/mini/Linux+NT-Loader.html
http://linuxdocs.org/HOWTOs/mini/Linux+WinNT.html
Cheers.
Jamie...