I have a roku and tv connected to the onyko via HDMI, when I view the movie info it always shows the input as PCM 2 channel, the output is whatever I set it for.
This is the case even when I am sure I am using a Dolby 5.1
Not sure what you mean by "movie info". If that's the output of a particular Roku channel then you won't be able to change that.
Is the Roku connected to an HDMI input of the receiver and the HDMI output of the receiver to the TV? If so then check the audio menu of the Roku.
If the Roku is connected directly to the TV then check the audio settings of the TV as well.
Set the receiver to Dolby which will default to Dolby PrologicII if it sees a stereo input.
The front panel of the receiver will often indicate the input that it is receiving.