There was a comment in a thread somewhere about the real aircraft would empty tanks based on pressure differential of the pump. If one pump was a little stronger, it would overide the others. This does not occur in FSX. I normally keep the bypasses closed (Horizontal) and all the pumps on so the engines will draw from their own individual tanks. If I need to balance the fuel I combine the tanks (move valves vertical) and turn off the pump of the tank I do not want to draw from, this causes both engines on a side to draw from the tank with the pump on. The same can be done for the Aux and Ext tanks. Put all the valves on a side to vertical then turn off the pumps on the tanks you do not want to draw from leaving the Ext or Aux tank pump on to draw only from that tank till the level drops to where you want it. Be careful about the valves and switches, as in, don't turn off a pump until you verify another pump is on to replace it. If you turn a valve off and the pump off that engine will have nowhere to get fuel from and die :0

I normally separate the right and left system with the center valve to the off (horizontal) position.