* Will the system benefit better installing the 500g ssd drive and the 3k HHD at the 2 brown Intel SATA port or the Marvel grey port? SSD its big enough to house OS and apps/games. HHD will have media files and backup.
The Intel ports as they'll actually operate at 6Gbps. Marvell's probably does operate at 6Gbps but it's gimped because it's connected to the rest of the system through a slower bus interface.
*should I have windows catch on for the SSD drive on?
You mean the swap file? Yes, just reduce it to something like 1GB. Some programs don't react well if the swap file is missing.
*I noticed the i7 4820k can be run at a faster clock on turbo but at default its running at lower speed. Do you have specs for the Bios input on your Dec 2013 build so I can set it up and get same results as you? I am not scare of the Bios I just don't know enough.
Adjust the BCLK or multiplier.