What is your source component for stereo listening, and what is it's connection to the Nova Pre, analog or digital?
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Home theater bypass is often just unity gain. That is, the pre-amp passes the signal through without amplifying or attenuating it. Some pres simply switch the input to the output, bypassing everything.
You can simulate the first situation by simply connect the analog pre outs for the front spekakers from the Onkyo to the AUX input on the pre. Then set the volume on the pre so you get the appropriate level to match the fronts to the other HT speakers. You can do this either using the volume control of the pre or the volume adjustments in the HT setup on the Onkyo or some combination of the two. When you have the volume correct, simply mark the volume setting on the pre and whenever you want to use the Onyko for HT then select the AUX input on the pre and set it the pre-determined volume level. You can also rerun the room correction process on the Onkyo once you have things set up.
I think the Nova pre only has 1 analog input (AUX) so this only works if your other source inputs are digital. If you got that pre, I assume you are mostly using digital inputs. If you have a second analog input, you could put that through the Onkyo to the pre and use what direct or pure setting the Onkyo has for 2 channel inputs. Not as good as going direct, but it gives you the extra input if you need it.
If you are using your Blu Ray player as a CD player,you should be able to connect its digital COAX output directly to the pre, while leaving the HDMI to the Onkyo for HT, assuming the BluRay will output digital while the HDMI is plugged it. You could also probably just take the coax digital out from the Onkyo and pass it to the pre. Hopefully that would be a pretty straightforward pass through.
In the future, if you want to use an external amp for the center and surrounds, just use the analog pre-outs on the receiver and feed them to the external amp. Use the normal procedure on the Onkyo to set the volume levels.
It takes a little to get use to this type of setup but it is pretty straightforward. Just remember to keep the volume knob on the pre at a low level to start with.
If you want to go this route, please free free to ask questions.