I feel for you Shane! Top picture, the piece on the riser has been oriented correctly on your saw, the one on the tread has not. Look at the molding closely to see if there is a top and a bottom, one side might be wider than the other, the wider side might have a thinner area at the bottom of the cove. Put a mark on the tops so you don't get confused. If both sides are equal, just pick one edge as the top. The top goes against the wall when installed but the tops go down on the saw's table when cutting, you swing the saw to the left for the piece on the riser, swing it to the right for the tread piece. Always keep the top on the saw table. The edge that fits against the wall should be square to the wall. You can see that in the top picture on the riser piece, the tread piece in the top picture is 45 to the wall, not square. Forget about coping, you have to figure out how to be consistent with the molding position.
You have another thing to deal with, the tread nosing/overhang. Don't know if you plan for the cove to be continuous. Any reason why you don't go with wall to wall carpet on those stairs? You wouldn't need any moldings.