Yes, they upholstered over the holes and then we just sliced and folded the vinyl into to the hole and glued it to the wood.
Then we used a couple of L-shaped brackets and a large hose clamp on each of the cup holders to clamp the cup holders in place.
Basically, we clamped the L-shaped bracket to the side of the cup holders. The brackets butt up against the top of the console keeping the cup holder cups from pulling out.