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Is there a preferred way to use the SATA ports to get the best/fastest setup?

I have an Asrock x99m Extreme4

I'll be running 3 SSDs and a DVD burner/player

Also, what's the difference between the SATA & S_Sata ports?
 

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The "S" stands for "Shared". According to page 4 of this motherboard's manual, S_SATA_3 is shared with the eSATA port, and S_SATA_2 is shared with the Ultra M.2. Socket.

Fortunately, I am seeing no indication in the manual that this motherboard has any third-party SATA controllers; all are controlled by the X99 chipset, which is a very good thing. This means that you should be able to use any of the SATA ports with equal performance.
 
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