There is a way to avoid having the boot loader on the same drive, but its a little tricky.
First, your bios has to support selecting which disk to boot from.
Install each OS without the other disk connected.
Put the Windows disk first and then the linux disk. Windows should now boot normally.
Try booting the second disk, if it is using the UUID instead of the device id it should work. If not you are going to have to modify the boot loader to point to the correct disk now and then you should be set.
One other suggestion is to start a new thread for a new question, numerious reasons for this.
ralyon