If your connecting flight is within 24 hours of your first flight on the itinerary, you can check in for both flights at the same time and assign seats.

With NGCW, there is a 'window' in between the seats, so I would stick with the window pairs on the main deck (or preferably the upper deck if on a 747). The walls are indeed higher on the NGCW seats, but the gap is perfectly sufficient for chatting.