Kneeling can be tough for two reasons: Achieving the max range of motion is required for kneeling also a lot of people do not tolerate the pressure onto the knee.
The clicking and popping is due to the components (tibial and femoral)coming into contact. This can sometimes be due to increase laxity of the ligaments on the side of the knee (collaterals). I've heard some surgeons say that with increase quadriceps strengthening the clicking will minimize. My mother had to have a revision of the tibial component which helped out drastically. I'd still ask the surgeon.
Not only should you shop around for your therapist you should shop around for you MD. Makes a HUGE difference.