For OS X nothing special has to be done it just boots, however for Windows via Boot Camp it would not initially boot successfully. This allows connecting the sleds to the SATA III PCIe card. I did this by getting a PCIe SATA III card with a miniSAS to four SATA connectors cable, and also getting a kit to replace the drive bay sleds with special ones that bypass the normal drive bay SATA connectors. If you use the standard built-in drive bays then of course Boot Camp will work fine, I however as part of my project to upgrade a Mac Pro 5,1 2010 model have 'converted' my internal drive bays from the original SATA II, to SATA III. I use a standard SATA drive for my Boot Camp drive however I did encounter something on that front which might give you a clue. (Which is a genuine Apple 1TB SSD on a PCIe adapter.) I have not tried installing Boot Camp on my main SSD drive.
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