It sounds like you don't have a single bootloader to control both operating systems - i.e. Windows is using its own bootloader and Linux is using its. In order to have a choice between them, you'll need to be using only a single bootloader which recognizes btoh operating systems.
Probably the simplest method is to boot into Linux and edit your bootloader configuration file to add a section for Windows. Do this by opening /etc/lilo.conf in a text editor (as root). Search around here for the appropriate config section for windows, but I believe that adding
other = /dev/hda1
label = Windows
to the bottom of the file will do it, as shown
here. You might also want to alter the line that starts out "Default =" - this controls which option is automatically selected when you start up the computer. Set it to the label of either Windows or Linux, depending on which you prefer. Timeout controls the length of time the system will give you to hit the up or down arrows before it automatically boots whichever your default selection is.
Once lilo.conf looks like you want it to, run /sbin/lilo (also as root).
Then install both hard drives again, Windows as master and Linux as slave. Reboot, and you should be good! (I say Windows as master because of this line: "other = /dev/hda1".../dev/hda1 is the first partition on the master hard drive).
