You need more harddrives for efficient video processing. Its suggested 3 minimum and 4 optimal.
3 drives: OS/Programs/Source, Scratch, Destination
4 drives: OS, Source & programs, scratch, destination
Up to 32gb ram.
Also an AMD GPU if you plan on using GPU processing as Abode has dropped cuda support with CS6 in favor of opengl and amd's just kick arse in that department. Which also places more emphasis on making your hdd systems as fast as possible.
I suggest you read up on whats optimal for drives in your favorite editing forums.