Most gaming / performance MBs have 2 SATA controllers (like AMD/intel): a primary one usually with 4,6 or 8 SATA ports and a secondary one (like a SI).
The primary ones are faster and have better driver support.
My recommendation is to have all HDDs on the primary one. SSD also, except the case if you have a special SATA port for SSDs like a few recent MBs support. All optical units (CD/DVD/BR) or non-permanent HDDs (like a backup HDD you connect from time to time) should be on the secondary controller.