what you can do is put the drive you want windows to be on as the primary master. make the 3Gb one into the master, and the 20Gb one into the slave. Then the install will likely be the same as if you were using partitions except you will be using drives instead. If you are using LiLo, and if the installer sets up the partitions for you in a nice easy graphical way, and if your drives are all plugged in and the jumpers are all set correctly, then the procedure should look incredibly similar to you installing it as it did when you used partitions.
edit: by the way, i suggest that you make /home into a seperate partition from the rest of linux at install time, so that if you decide to hose your system for any reason, your home directory will be untouched. The same goes for My Documents in windows. Make it a seperate partition.
[ November 04, 2002: Message edited by: Calum & his insidious little spies ]