Hey, good morning!
In terms of getting audio from the blu-ray player, I'd say go into the Marantz menu and make sure that the input that you are using has been assigned to the source that you select (on the remote or front panel) to watch the blu-ray. Page 28 of the owner's manual discusses assigning inputs to sources. I can't see where you'd need to assign the video and audio separately (some receivers are like that), so if you get picture - I'd assume that the audio should be assigned as well.
I think that I saw in the manual last night that the Marantz can handle sampling frequencies up to a certain level, but I can't remember if that was over HDMI or not. If assigning it doesn't work, let us know.
I'll look into the sub issue. I just need to go walk the pooch right now, but I'll be back in a couple of hours.