DVI and HDMI are very very similar, either will be fine.
VGA is of a lower quality tho.
For crossfire, you have to use outputs on the top, or "master" card.
As for the "closest to the motherboard" that doesn't really make any sense. Graphics cards are full of complex circuitry and no signal will go direct from mobo to output, but even if it did, the signal quality wouldn't really be affect. At most the only thing that would change is the time it takes for the signal to pass through the circuits, but even then were talking nanosecons or maybe less, maybe picoseconds. Regardless, it's a silly thing to consider.