IMO put your OS on the 200gb, put your data on the storage drive. what works on windows 7 should work on W7, if not, run it in compatibility mode and it should work. migrating to W7 should be a breeze and smooth transition.
To answer your question, just make a "Backup" (something like that) folder on your storage drive, and put ALL, and only your data there... keep operating system and data drives separate. you dont want to lose your data when your OS dies