Bodyweight excercises are a key element in any workout, NGR or otherwise. I have a gym full of high end equipment and I use at least one bodyweight move in almost every workout. For me the most important thing to remember whether it's a squat, lunge, crunch, pushup or any variation of them - is to FOCUS ON THE MUSCLES YOU ARE USING.
If you are squating think about feeling your glutes (Butt) working, if you're not and just feel your quads (front of the thigh) you're doing them wrong.