I like to put the two batteries into the RX via the two ports that are on either end of the receiver, that way the load is spread out over the whole RX bus. Not really sure it's an issue but since I can reassign channels wherever I want with my SD-10G, I do it. You could also just Y-harness them into the end channels as well without any channel reassignment. And yes, both batteries need their own switch.
I prefer the HD chargeport switches. We alter the switches by removing the signal lead going into the RX then using a standard ailerion type connector coming out of the LIFe batteries we can balance charge the LiFes through the chargeport switch. Not my idea, recommended by NoBs batteries. Works like a charm but we label the planes with battery type and capacity at the switch so we know what's in the plane.
Wit