If you're not interested in making a RAID, then I'd suggest considering connecting one drive to the Intel-based SATA3, and the other to a GSATA port.
Since the main (only?) difference between SATA and "GSATA" is that "GSATA" uses a separate on-board controller (the Marvell; separate from the Intel chipset).
This is why I suggest using one of each, as it will give each drive it's own controller, data path, etc.
On the OTHER hand, turning off one of the controllers (ie: the GSATA one) may free up enough resources that having both drives on a single controller may be the 'speedier' option.
Personally, I'd turn off the Marvell and just go with the Intel for both drives, one less driver to care about.