The Marantz gear you acquired is a Pre/Pro. It is a Preamplifier with Processing capabilities. For the Marantz to play one sound on your speakers to play, it must be connected to a a set of external amplifiers... If you have 7 speakers, regardless that they came as one or several boxes, this or these amplifiers represent a total of 7 channels .. TO make things simple, the subwoofers usually have built-in their own amp....
Your Onkyo Tx Nr686 is an AVR, an Audio Vidéo Receiver, It has a Preamplifier and the required complement of amplifiers built in... plus a tuner, a thing to receive radio stations.. thus they call this a Receiver...
Your Onkyo can decode Atmos, but it has only one stereo Line output i-e, one left and one right, It doesn't have 7 or more output outputs, one for each of the channels it is capable of decoding. We're not counting its subwoofer output in this ..
Simply put : You can 't use the Onkyo with the Marantz.. It is one or the other:
Option 1: the Marantz, perhaps a better unit , perhaps; with a set of amplifers to power the speakers. Please be aware you wont (can't) enjoy Atmos decoding.
or
Option 2: Your Onkyo that, by its lonesome will power the speakers and do Atmos...
You can't use Both...
Solutions:
1) Return the Marantz and you have Atmos decoding capabilities, keeping in mind you will need a new set of speakers for the Atmos-thing... or
2) Return the Onkyo , buy some amplifiers for the Marantz.. NO Atmos, no way. You need additional amplifiers, if you ask here, we will gladly suggest some to you... But you can't and won't have Atmos.
Peace.