Imagine you're trying to talk to someone while a cannon is firing near you. You can't do so because the bass from the cannon is too loud relative to your voice. That is the first thing you generally need to do with a subwoofer: make sure the volume matches your speakers' volume, so that there's balance and is not too loud.
The vibrating windows or floor problem, that's because the subwoofer is usually tuned to play some frequencies at a volume that's too loud (too high SPL) to impress prospective customers, but when you bring back home, it's too loud (too much energy) and your glass windows / wooden floor resonate and vibrate in response. You can generally control that by adjusting the subwoofer volume, and the crossover frequency that most competent subs have. For advanced adjustments you can use EQ and adjust specific frequencies that causes vibrations in furniture, say 60hz.
Through research, most people generally want bass (20-100hz region) to be somewhat higher than the rest of the sounds from your speakers (100hz - 20khz region), but not too high like the cannon vs your voice. Something like the black line for 'All Listeners'. You can also compare this graph below to the MR3 graph earlier and hopefully you can see that the bass level that is preferred in the research, can't be achieved by MR3 because its performance drops right after 70hz.
So we have to use a subwoofer to fill in that gap.
But again, we don't want it to be too loud, so we will do the balancing with a measuring microphone for best accuracy, or you can also use your ears. But instead of listening to random music, we use a frequency sweep up to 200hz. As the frequency sweep plays from 20 - 200hz, you
ideally want to hear a constant or higher volume at 20hz then gradually decreasing volume. But in reality, A) our ears are not that precise, AND B) a good subwoofer that can play loud at 20-40hz isn't cheap (and not small) so if you can get the bass frequencies sounding roughly as loud as the frequencies above 100hz (from your speakers), that's already a good home set up. Usually for affordable subs like T5s they play down to 45hz.
The placement of subwoofer can also affect its performance in another way.
You probably already know sound waves vibrate air molecules and your ears hear these vibrations. An analogy will be the ripples and waves when you drop a rock into a pool. When you throw a larger rock (bass) into the pool, the ripples become larger waves (stronger air vibrations). Then because the waves hit the walls of the pool (and your room) and get reflected, these reflections will cause some waves to rise higher at some spots and drop lower at other spots. The net effect is that you'll hear louder or softer bass notes when you stand at certain spots in your room. These are the room modes, or the peaks and nulls, though you may or may not notice the problem.