Yes, they are connected in parallel. If you open the top panel of the amp, you can see that the + and - connection of the second pair of speaker binding post are "tapped" to the first. So in essence, it does not matter which set you use, they are connected in the same "point " in the output circuit, thus no set is better than the other.
I believe that you will not have a problem if you connect the other post to a speaker selector switch. If you are listening to 2ch, the switch is open so there is no load except your primary speaker on the other set. If the switch is activated (ie. 2 sets of speaker now) the only concern is that your load will be in parallel, making the impedance to be lower (or half if the speakers have identical impedances). The result is that it presents a tougher load for your amp because it will require more power to drive the 2 pairs of speaker( i.e 180 w at 8 ohms, 360 w at 4 ohms, ? watts at 2 ohms...etc.)
Hope this helps