So you can either set the bios to boot from the second drive, or you can make sure the bootloader is on the first drive. I'll assume you are using grub, not that it matters much.
You'll need to boot a live cd, mount your linux partitions hierarchically and "chroot" to the linux root partition ("man chroot" tells you more). You then run grub and tell it to install on hd(1). (I'm assuming that your second hard drive is slave on the first channel. If you have a CD ROM drive, this will be the case 99.9%.) I suspect grub will provide enough help to allow you to figure out how to do this, otherwise there are resources on the web.
Samsara
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