Bill, 

Since Charlie hasn't posted any pictures or sketches of his design, I was referencing more what you'll find in auto installations than in a/c.  Still the principles are the same, namely that the coolant naturally flows to the bottom and air goes to the top.  If it gets low enough, the pump will begin sucking air and will soon loose prime.  This will happen much quicker if you're drawing off the upper tank.  Of course, if the radiator is located below the engine it will take longer for this to happen than if it is beside the engine because the air pocket will be inside the engine rather than in the radiator.  If you have a coolant leak in flight, you'll benefit from more time to get on the ground rather than less. 

I don't see where it makes any difference which tank you return the coolant to, but when supplying the pump, any air will risk loss of prime.  So, it makes sense to me to draw from the bottom and return to the top.  At least that's how I understand it.

 In the end its Charlie's decision.