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There are two ways that a movie DVD/bluray will play bass (depending on how it is mixed/engineered). Sometimes bass effects will come from the left/right channels. In that case, they will be sent to your left/right speakers if you have set your left/right to be "LARGE" with no crossover.
Other times, bass effects will come from the ".1" LFE channel of the movie sound mix. In this case, it will only be sent to the subwoofer, unless you have the subwoofer disabled on the Marantz. If you have no sub, the bass will be sent to your left/right speakers.
I have had movies that use both left/right channels as well as the ".1 LFE" channel for different bass effects. In your case, you could set the left/right speakers as "LARGE". Or you could set them with a very low crossover point such as 40hz or 50hz. This would allow the left/right to play most of the music low-end, but the Marantz would still send very low bass effects to the subwoofer.
The manual for your receiver appears to be quite extensive including an appendage for the Audyssey equalization as it pertains to home theater use. After a cursory look I didn't see the ability to set up multiple equalization settings which is not to say it doesn't exist.
I find the ability to adjust the subwoofers parameters by remote control from the listening position in my music only system incredibly useful with some recordings. The Velodyne Digital Drive Plus line of subwoofers offers six multipal preset controls. They can also be used for a separate HT or music only system connected at the same time but used by one or the other while in use. There may be other brands that do this that I'm not aware of.