Agree with the suggestion of using only the main L & R for music. Using the same setting for the subwoofer for both music & movies is doomed to disappoint; most subs can do either, but not both without different settings. There should be user presets on your Marantz that changes settings (low/high pass & level) depending upon the source and/or type of source, ie 2.0 vs multi-channel.
Some people find audio over HDMI is a bit edgy compared to S/PDIF, but most do not. Good luck and welcome to the forum.