Hi. That's a nice setup that you've got there.
Sounds to me like you have at least your front speakers set to "Large," which would mean that bass from the front channels would not be sent to your sub. If that is the case, setting them to "Small" would send a signal to the sub even for 2.0 audio from sources like YouTube. If you haven't already, go into your speaker setup menu on your Marantz and make sure that the speaker crossover settings are what you want. With your speakers, I think that you'll want to at least try setting them to "Small" and let the sub handle the lower frequencies, as none of your speakers will play as low as your sub.