If you can boot that second drive, hopefully with a Linux boot disk that you made during install, then its easy. Just use that to boot into linux, and then re-run the boot loader. Either from the command line with: /sbin/lilo, or /sbin/grub (depending on the boot loader).
If you don't have the boot disk, use an install CD and boot with that. Ignore the graphical cute install crap and hit ctrl+F2+alt and you've got a shell. Then you have to mount the Linux drive's root partition. Assuming its the second hard drive on the first IDE controller and that the root partition, / is the first partition:
mount /dev/hdb1 /mnt
Now you've mounted the Linux drive and switched to it being your root partition. Now you should be able to re-run the boot loader. It'll write the boot loader back to whatever it was.