it's really completely up to you... you could go the way of using one disk for windows and one disk for linux, but for the operating system you'll be using the least it would be a waste of space, perhaps.
just to give you an idea, if i personally had two 80gb disks and had to install windows for some reason, i'd give the first 20gb or less on the first disk to windows, the remaining 60gb for the linux root, swap, and home, and i'd use the second disk completely for storage (linux)... i'd use the reiser file sytem for linux and fat32 for windows because fat32 is at the present time more reliable to work with from linux than ntfs... and also i'd keep a tarball of my windows partition in my linux so that when a virus or an a-hole shreds my windows box i can have it up again like new in a few seconds.
of course you could assign windows more space than linux if you just want to tinker with linux on the side and plan to do all your main stuff on windows... either way, the choice is yours. and you have MANY CHOICES.
ah, open source.