I'm currently battling with the same issue, my setup is:
-Roku 3 to HDMI IN on the HW550
-HW550 HDMI OUT (ARC) to HDMI 2 (ARC) on the Samsung 55F6400
Sound is good, however I am also frustrated by the fact that I have to use the soundbar remote just to change source to HDMI because it defaults to D.IN every time it is switched on.
I am thinking of trying the proposed setup (Roku 3 to HDMI 1 on the TV, HDMI 2 (ARC) to HDMI OUT on the HW550, but concerned I will lose out on the "surround" sound (as the soundbar will be getting stereo signal rather than the DD/DTS).
Am I correct in assuming the above? Will the sound output be inferior this way? In fact, if the soundbar is getting a stereo signal, then I may as well go back to the SoundShare (Bluetooth) wireless connection?