Sabertooth X79; 1 each, 1TB HDD for Windows 7 Professional 64 bit OS; 1 each, 1TB HDD for Programs; 1 TB HDD for Scratch Disk, 1 each, 2TB HDD for Files. Does it matter whether the OS HDD is plugged into the Intel SATA 6Gb/s or the Marvel connections? Does it matter which 6 Gb/s SATA connections are used for any of the 4 HDDs?
In a way it does, in a way it doesn't. the Intel SATA Controllers tend to be Similar enough to one another that, for instance major system failure in the future, you can swap the board for another intel chipset board, and boot it up just the same if you install your OS to a SATA port controlled by intel. if you go from Marvel to Intel or god knows what else they pop onto a different board, Windows will BSOD.
My verdict is to install OS on the intel. the rest is fair game.
I prefer the Intel SATA ports and IF the "1TB HDD for Windows 7" has a SATA3 interface then use the Intel SATA3 port -- you'll get a smidge better performance with larger cached disks, and after the install Enable 'Write-back cache'. The Intel ports IMO are more reliable than Marvell.
Afterwards you can change the SATA -> AHCI if you'd like, but that method is the only way IF you want the Intel RSTE drivers to install properly and/or IF you ever plan on any form of RAID in the future.