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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