NUPRIME IDA-16 Integrated Amp setup

If the majority of your listening is to music in stereo then I would plug the pre-outs of the Nuprime into the Denon and then just turn the Denon on for movies and to power the center  and hook the other gear into the Nuprime.  It really just depends on your usage and what your auxiliary gear is.  For stereo listening the Nuprime is going to beat the Denon in every way.  If the majority of your usage is for movies then do it the way you planned.  I would also try movies with just the left and rights connected to the Nuprime and see how that sounds.  After years of multi-channel set-ups in my FR I finally sold all that gear off and am running a pair of Spatial open baffle speakers with subs using a Nuprime DAC-10 and ST-10. 

@jackd

I appreciate the response! My primary goal is maximum music quality. That being said the majority of use the speakers get is from the television or movies just because the system is hooked up in my living room.

How would I transmit music/movie audio to the IDA-16? The reason I use the Denon is to stream from my computer or phone.

Unlike any AVR I have ever owned yours has no main analog outputs at all only zone 2 and subouts so no way to connect it to the Nuprime that I see. Connecting it the other way is a waste of the Nuprime's capabilities.

@jackd How about the Marantz 6012? This is the AVR I was planning to wait on but will pull the trigger now if I need to.

Still no analog outputs and as Denon and Marantz are the same company not surprising.  If you only have the three speakers what are you using the AVR for other than the built in streamer and the center channel?