Originally posted by Ares
Speaking for myself here, i would throw the OS on the smaller hd and set that one as Master.
I agree with Ares,
Use the smaller drive as your system drive (OS, Applications)
and use the larger drive as storage!
Usually programs benefit from this type of configuration, for example, if you Photoshop, and you have two seperate drives, your process time is dramatically reduced!! (Photoshop calls it scratch media)
Plus, if your OS drive crashes, you won't necessarily loose all of your data on the other drive!