To get two drives to work together you must make sure that one is set as the "master" and the other the "slave" (not kidding!). This is usually a jumper setting. Typically the master is assigned the first drive letter.
If you want to boot from the "master" one day and the "slave" the next, you can easily change the boot order in the Setup (BIOS). IDE Drives (the kind you most likely are using) are assigned numbers 0-3, 0 being the first one (again not kidding. It is binary reasoning).
If you don't want to boot want to change the boot order in the BIOS there are ways to set-up multibooting on the main drive through software or clever installation techiques.
Another neat solution to multible Operating Systems is of course Virtual PC.
That is: If you don't want to change the boot order...