You just make sure that both the sub and the shuttle have power lines connected to the docking port itself. Those will transfer power between vehicles.

Just run a power wire from docking hatch to battery array you want charged.

Pooling batteries is as easy as running them all through a relay to a single power out. Then they are effectively pooled. Junction boxes also pool power inputs, with far fewer output connection potential obv.

Just dont do a few things with batteries and relays. Dont do relay to relay power, doesnt work. Dont connect battery to battery directly in a daisy chain. And dont allow a battery to charge itself or you will get power pulsating that fries your junction boxes.

Also dont do reactor -> relay -> junction boxes. Some reason that makes a lag generator.

That answers my question, thanks!