Hi!
If you buy a new motherboard, you shouldn’t have any problems.
USB 3.0 problems are more typical with systems which are maybe 2 – 3 years old as USB 3.0 has improved a lot and the drivers are not automatically updated by Windows update. So what happens is that the drivers installed are maybe 3 years old and they can’t keep up with the actual USB 3.0 bandwidth, which e.g. the Tobii EyeX requires.
However, there are a few cards we have tested so you can have a look in our Support section: Supported USB 3.0 pci express cards
/konstantin