Changing hard drive configuration.

There is no such thing as a SATA 6Gb/s HDD. Unless you meant a SSD? No conventional HDD comes even remotely close to maxing out the bandwidth of a SATA 3Gb/s port, so there is no reason to have them clogging up a SATA 6Gb/s port (save them for SSDs), so DS was correct in doing that.

What HDD and motherboard are even talking about here? If it is a P67 motherboard then there are 2 Intel SATA 6Gb/s ports and 4 Intel SATA 3Gb/s ports. Some P67 motherboards additionally have 2 Marvell SATA 6Gb/s ports tacked on, or at least they're advertised as such but in reality their performance is god awful bad and you want to avoid using them at all costs as long as you still have Intel 6Gb/s or 3Gb/s ports free. If it is a X58 motherboard then it has 6 Intel SATA 3Gb/s ports. Some X58 motherboards additionally have 2 Marvell SATA 6Gb/s ports tacked on, same deal avoid them.

If your HDDs were installed using Intel ports then I highly doubt you can just plug them into the Marvell ports, they aren't configured for it. Same thing if you have Windows installed under AHCI mode and then switch the motherboard over to IDE, you won't be able to boot because only the AHCI drivers are installed, and vice versa. However if you are just switching from an Intel port to a different Intel port I wouldn't think there would be a problem, but I could be wrong.

I have an EVGA X58 Classified 3 (141-GT-E770-A1). The spec sheet says the SATA III ports use the Marvell 9128 controller. Are those the bad ones you're talking about? What makes them so bad?