I live in a second-floor apartment and I have a down-firing 12-inch sub in my living room HT. Some facts: my neighbors are seldom around, and the walls of my apartment building are really well-insulated; also, all my listening spaces are pretty small and I'm not a true basshead like a lot of the other guys who post here, so my system's typical output levels are pretty low compared to most other posters'.
I've used an Auralex SubDude for most of the last nine months. To my perception--I have taken no measurements to corroborate--it *does* reduce some of the room vibration. I had no random object shimmies to start with, but after installing it, I perceived a difference in visceral impact. There seemed to be a change in the relationship between the amount of bass I felt and the amount I heard; with the SubDude installed, I felt less and heard more.
Recently I removed it, and returned it to its box in a closet. All things considered, I prefer feeling more of the bass. As for owning a sub in an apartment, I think there's no one-size-fits-all rule; I'm lucky because my walls are thick and my neighbors aloof. Some apartment dwellers aren't so lucky. I think you need to pay attention to things like whether you can hear your own bass when you are in the hallway outside your front door, or what it sounds like outside one of your windows (better yet, of course, if you can hear what it sounds like when you are in the downstairs apartment--bake a pie and introduce yourself
Also, my HT receiver uses Audyssey Dynamic Volume, which narrows the dynamic range of program material. When it's enabled, speech and other finely detailed midrange sounds are clearly intelligible at any volume, and yet I don't have to dive for the remote just in time for the underwater nuclear explosion earthquake cannon barrage crescendo. You know, the one that always comes right after the long whispered conversation full of essential plot points. Purists object, and I get their point, but for my money, this feature is a godsend. Your Yamaha has a Dynamic Range Compression option that should function similarly; I think you should try it and see if it helps. Good luck!