I had such mixed installations before, have installed Linux, win NT, win98 on the system and could pick any one during the booting. Later found this method is not good. If the MBS got problem, all systems will get trouble,
If you installed your two disks independently, you should not have this problem.
I suggest that you go ahead to install OS on your new disk and make at least 40GB as the system partition. Leave the rest 160GB to be formated after the system is up.