[Motherboard question] got my hands on a XFX ATI Radeon 6990 HD

docetes

What would the difference be if I put it into a cheapo board like this instead of a pricey one like this

Mister Man

To start, the expensive one you listed is for HTPC normally (Or a very small PC) It's pricey because it's small.
The cheap board you have there is ok, not great. It doesn't have USB3.0, Which is started to come on most boards, but you should be fine without it. It also only supports a single GPU, so you won't be able to add another 6990 if you ever plan on doing so.
AM3+ I Believe is being released now, not many places have them, so you won't be able to upgrade your CPU when AMD Move onto the new socket.
You should be fine with the cheap motherboard for now I think. Unless your looking at a really small case, stay away from the tiny motherboards.

t1mm

You might want to look at a board with more than two ram slots - I would imagine you'd want to fill the computer up with RAM to benefit from the GPU's full potential.

docetes

Thanks for the quick reply. Where does it talk about the GPU support?

Monotype

The more expensive one is very small in comparison and it already has a processor in it.
How much money are you willing to spend? Do you need everything apart from the GPU - Case, PSU, Windows, Keyboard, Speakers?