There is one other thing to bear in mind. Many modern motherboards have some SATA channels as part of the core chipset (say the Intel part, ICH9-R for example, for a nominally Intel chipset) and an add-on that may add some PATA ports, RAID, e-SATA or something and that's likely to be a chip from a third party supplier.
If you have one of those, you will almost always find that the ports from the core chipset better supported and better detected at install time than the aded-ons. So, if you use the ports from the core chipset part you will make your life easier.
I'm sorry, I can't offer you a general rule to tell which are which (the connectors may be in two groups and they may be of different colours and the add-ons may be close to the add-on controller, but note the word 'may'), but the manual for your board will tell you more, and that may make things clearer. Oh, that word 'may' again.
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