if you setup the RAID on the nVIDIA controller for Windows, you can't use the SI for Windows. no, connecting the cables to the wrong controller wont hurt it, as long as you don't connect both ports on the same controller together. I will always put number one HD higher in the cage ,then two ,etc. so I always know wich is wich. You will have to reinstall windows on the SI controller if you want it to boot from that controller.
Biostar T-force 4U,Opteron firstname.lastname@example.orgGhz.CorsairXMS DDR500-2gigs,EVGA7800GT CO.Seagate160gigSATA II,Koolance ICM 510 watercooling,Coolermaster Stacker830