There are tools you can use to precisely calibrate your subwoofer(s).
But, here is my take on this:
Music is more directional as the frequency increases. And, more omnidirectional as bass decreases. Natural bass notes have harmonics. The deepest bass tones will be directed to the sub, harmonics will find their way into the mains. Your ears and brain try to detect where the bass is originating from, which is going to be the higher frequencies in the spectrum. The goal here is to try to trick your brain into thinking the bass is coming from the mains and not the boxes located somewhere else in the room. This requires a combination of setting the crossover frequencies and subwoofer output to reach the best result. Too much gain and/or too high a crossover frequency will direct your ears to the boxes that contain the woofers. Depending on how loud you play, I try to place the responsibility on the mains to play as low as they can play and still sound clean, undistorted, and effortless and set the sub crossover accordingly. This gives the smoothest transition from low bass to the mid bass and makes your mains appear to magically have a couple 12" woofers in them.
It’s trial and error. The number of "clicks" required is difficult to predict. Good luck.