I dont know the proper way to do this as I dont have a dual boot, buut, in the BIOS (usually you get to the BIOS by holding delete as the PC powers up) you can choose the boot device. If you want to always boot from one drive you can set it so that is the primary boot device and that will be the one always used. Otherwise you can just go into the BIOS and choose which is the primary device every time you change your mind.
Also I know that when I accidentallt installed win98 and win2000 on the same drive the windows startup always gave me the iopion of which to boot to. I dont know if the same applies when you use 2 drives though.