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First decide What OS will be your primary OS. What OS do you think you will need the most space for? If you play a lot of games then use the big 200 gig as your windows disk cause you will need more space for your windows games.
I cant quantify how much slower the hdd will get if you are sharing it with another device, but I guess this would only happen if you were accessing the cd-rom at the same time. Also do you really need 3 hdds? why not just use the 200gig for windows and the 60gig for linux. Wouldnt the slow down also happen if you are accessing 2 hdds simultaneously which are connected to the same cable?
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