since you installed Debian in the 2nd drive, I assume that you put GRUB there also. I'm also assuming that---with the 1st drive connected--you can still boot Windows.
You have at least 2 options:
1. If the BIOS can be configured to select which is Drive #1, then you can do multi-boot that way.
2. Do whatever you have to to get it to boot from the Linux drive--eg you might simply switch the cabling/jumpers.
Once you are in the Linux system (by any method), (IF GRUB IS NOT ALREADY ISTALLED) then install grub like so: (I'm assuming 2 ide drives--#1Linux, #2 Windows)
grub (starts the grub shell)
root (hd0,0) (tells grub that it's home base is on the 1st drive, partition #1**)
setp (hd0) (puts grub in the mbr of drive 1)
Now, you need to configure grub so that it will boot windows:
open /boot/grub/menu.lst with a text editor
Create (or edit) and entry that looks like this:
map (hd0) (hd1)
map (hd1) (hd0)
The two map commands are required because you have Windows on drive 2.
**Note that grub counts from 0....