IMO, you have already received good advice on this thread. In my case, with two large Aerial SW-12 subs, I would invoke the 80/20 rule and say that they sound just about optimum on about 80 percent of tracks that I listen to. However, I have them dialed in at just barely above the roll-off frequency of my mains, and at just about the minimum acceptable loudness, so that on many of the tracks where they are not optimal, the errors are omission (slightly less than optimal bass loudness) rather than commission (i.e., boominess). Even though my room is moderately large, I had the boominess issue with about 40/50 percent of the music I played with my former large, bass reflex speakers. Moving to more moderate sized acoustic suspension speakers (two 9-inch woofers in a sealed box) and adding the two subs allowed me to dial in a much more impactful and less intrusive bass response from my system.
Positioning and settings are certainly important, as pointed out by @soix, and moving to a slightly higher roll-in frequency and slightly lower output loudness can help (mostly) optimize the bass response over a wider range of your music collection. I am fortunate that Aerial chose to offer remote control operation of the SW-12s, since most of the time a problem can be solved by slightly increasing or decreasing the output level. In addition, I find that bumping the output up a notch or two when playing music at low volumes, or bumping the output down slightly when playing music really loud, can also help optimize the sound. In addition to the output level, the SW-12 remote also has toggles/settings (that I never use) for mute, EQ, and damping.
One last thing, look up the Audiokinesis Swarm Subwoofer System, which is a bass array using four subs. You don’t specifically need the swarm system but adding another pair of subs, or even just a third sub run in mono, may help equalize the bass response in your room.