Hello
I do this same thing with my sound room. I take the output from my Meridian HT system, front left & right to the proc input on the Ref3 then from the Ref3 output to the amps, This lets me be very flexable. This allows the Ht or Stereo to control it's own volume. With it this way you can also send the digital output from your equipment to the HT system & all the analog outputs to your stereo preamp. Then you see which sounds best to you and use the system that way. When you have people over you can use the HT and send sound to all speakers also.
The only thing you should do then in my opinion is optimize the room for 2 channel and use the digital abilities of the HT processor to adjust the HT part of the system. You also might want to cover your screen even one that is flat, with something when listening to 2 channel cause that way you will get a better imaging & a better sound stage between the speakers.
I do this same thing with my sound room. I take the output from my Meridian HT system, front left & right to the proc input on the Ref3 then from the Ref3 output to the amps, This lets me be very flexable. This allows the Ht or Stereo to control it's own volume. With it this way you can also send the digital output from your equipment to the HT system & all the analog outputs to your stereo preamp. Then you see which sounds best to you and use the system that way. When you have people over you can use the HT and send sound to all speakers also.
The only thing you should do then in my opinion is optimize the room for 2 channel and use the digital abilities of the HT processor to adjust the HT part of the system. You also might want to cover your screen even one that is flat, with something when listening to 2 channel cause that way you will get a better imaging & a better sound stage between the speakers.