My joints commonly crack, its not so bad has it used to be in hindsight. I would continue learning how to squat but i would advise you not to push the envelope to much IE light to moderate weight for 8-12 reps or something and see how it goes. Some people can't back squat heavy a lot, me being one of them. I front squat more.
One thing i have learn over the years is its ok to treat some lifts differently. For instance i never go over 5 reps on the deadlift.