I had to use the samsungs built in "Tv sound connect" with the 2 Samsung Radiator 360 speakers and then enable hdmi cec on tv and apple tv. This allowed the sound to controlled from apple remote and the tv settings allowed to make them function in left and right stereo. Pretty badass setup, everything works with one apple remote!
Yes, if you do the traditional bluetooth speaker pairing with apple tv, while they both will show connected via BT simultaneously on apple tv, sound will only come through one of them.