One battery gets plugged into the normal battery port. The second battery can be plugged into any unused channel. If you don't have a spare channel it can be connected to any channel with a Y. Both batteries need to be 5cell and on its own charging switch.

See http://hangtimes.com/parallel_packs.html

Yes, you can do the same with two Lipos. Each battery would need its own switch and regulator. I'd suggest using nicads or A123's and no regulator.

Joe