OK, the plumbing run that you did looks basically how I had interpreted/assumed earlier. I'm not following on the water flowing within the sump part. It doesn't look like you have any baffles in the picture. But I understand that you'll have the heater and pump towards the other end. Let me know if I'm missing a point.
I'm not certain why they would advise you to add a ball-valve on the dry stand-by. The only thing that I can think of is in case you wanted to do some sort of maintenance, but even then you shouldn't need the ball-valve. I'm not familiar with the glass holes version, but typically for bean-animal or Herbie, you'll want a gate-valve on the primary drain. You'll use this to control the water flow, which in turn sets the level for the second drain and as a result also addresses some water noises. The third should be completely dry.
I know it's not ideal, but you could add the values almost after the bulk-heads in the back and could access if you needed to make adjustments. If you had the PVC run horizontally under the tank, you could ad the valves there. But I think that adding pipe that's really not needed.
I hope that this helps, and, not causing confusion.
