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Are you actually referring to Intel Smart Response Technology (ISRT), where a SSD is used as the "cache" drive with a HDD? You didn't mention what mother board you are using, so I can't tell if you have that feature. That is a new feature only available on the Z68 chipset boards. All Intel 6-series chipsets have the two 6Gb/s ports as ports 0 and 1, so I don't understand how one of them is a 3Gb/s port. Does your board have another SATA chipset?
IRST (not used with ISRT) does not require you to connect a drive to any specific SATA port, and given what I have read about ISRT, that is still true.
Yes I'm sorry I am referring to the Intel Smart Response Technology. I'm using the Gigabyte z68xp-ud4 motherboard version 1.3. Updated to F6 BIOS version. Yes my motherboard does also have sata3 gb ports. There are 4 sata3 gb ports, 2 sata6 gb ports and 2 more Marvell sata6 gb ports. In all 0-7 ports. So from what you stated it doesn't matter which ports you connect the ssd and the hdd?