jdcranke07 :
cub_fanatic kind of touched on it. The only thing you would have to worry about would be how many PCI lanes you will be utilizing in your setup. Which with a X99 setup, you shouldn't run into that issue. Thunderbolt does nothing for you video at all unless you are using the Mini DisplayPort ability they have. Typically Thunderbolt will be utilized for data transfer since it is the fastest method for data transfer at the moment. And if the port is built into the motherboard then the port is meant for data transfer and not video unless the manufacturer specifies otherwise. But, it does not deal with SLI or CF in any way other than the usage of PCI lanes.
Ok I see. So not having Thunderbolt on the motherboard will affect Pcie SSD like the OCZ Revodrive (Which I kind of want) but not multiple GPU's.
I really want to get the Asus X99 deluxe motherboard but I guess I will not have full SSD Pcie functionality? Also I want to put at least 2 GTX 980's in it for SLI and possibly even 3 of them for Tri SLI but I can't tell if that motherboard would have space for it with a Pcie SSD... Can anyone make a suggestion for what motherboard to get for a Tri SLI setup with enough room and abilities to support Pcie SSD's? Thanks for all the info so far and sorry for such a noobish inquiry.