I trust most guy's here are doing the BB'ing version of the squat. Bar high up on the traps, shoulders back/chest out and in line with the spine and hips/glutes as much as possible for their body type. Even placing a 2X4, BB plates, etc under the heels will keep the body more inline when doing this exercise. Will also place more focus on the quads themselves. And reduce stress on the lower back. Squats are a primary leg exercise, not a lower back exercise.
If your grunting and groaning and the upper body is bent over, chest caved in, while the bar is resting somewhere between the middle and lower trap (or even half way down the back...which I have seen...looking more like a GM'ing exercise than a squat), than your doing the exercise totally wrong. And of course you lower back will bother you. Use a weight you can handle first of all,in a correct style, so the legs get the brunt of the work, not the lower back. And do them in the usual BB'ing rep range of 8-12 reps for awhile and see what happens to your quad development.Good Luck.