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I ask a lot of questions because I second guess myself... but here goes anyway.

I have zero 6 Gbs devices. I can ignore the Marvell SATA ports, disable the Marvell controller, and just use the standard Intel 3Gbs SATA ports for my system right? Seems to speed boot some to disable the Marvell controller. Am I screwing myself out of some sort of performance if I'm not using those ports?

Only 3 devices I have hooked up internally... the two HDDs from the Sweeter Spot (320 Series SSD and SS Spin F1) plus a DVD burner.

If you have a drive that has performance specifications faster than 3Gbps SATA then use the 6Gbps ports. Put another way, if you have a drive(s) that exceed 375MB/s in Reads/Writes then use the 6Gbps ports, otherwise you won't see any difference.

It makes sense to me that disabling the 6Gbps port would lower your boot up time as your machine wouldn't need to initialize the drivers for that port. Not sure if that's really how it works. Since all your drives have SATAII interfaces you could just hook them up to the 3Gbps Intel ports and ditch the Marvell controllers completely.

The intel controller also has 2 sata6 ports(white ports), so you can both use the sata6 and disable the marvell controller(and the jmicron).

Personally, I disabled Marvell, Jmicron. 1394, Serial and everything else I didnt use. Also had the Audio disabled until my Asus Xonar D2X went haywire and stopped worked. So I'm running on the HD-audio until the Xense arrives.