Shutdown your PC, make sure the connectors are properly seated (including power), then restart. In the BIOS, you want to be in AHCI rather than IDE mode (although the drive should still show up; you won't have TRIM nor best performance in IDE mode). If the drive still doesn't show up in the BIOS, you got a DOA.
You are connecting to the INTEL sata III port correct, NOT the marvel controller.
You need to set Intel controller to AHCI mode.
Disable marvel sata III controller unless you are using - Marvel controller OK for HDD (But should also be set to AHCI mode, not IDE.) But really very little advantage of connecting a Sata III HDD to SATA III port anyway.
I have the Non gen3 Asrock extrem4 MB and had no problems setting up a aggility III with windows 7. Just last week removed the agillity III and installed my new Samsung 830, again running smoothly. At work so can not access my Bios.
My current set up
Intel sata III port 0 - 128 gig Samsung 830
Intel sata III port 1 - 120 gig Agility III
Intel sata II port 4 - 1 TB samsung F3 HDD
Intel sata II port 5 - LG Blu-ray Writer.
NOTE: Your Intel port should be set to AHCI, NOT IDE and SMART should be enabled.
When you get to installing windows - DO A Custom instal and DELETE all partitions you have created!!