I am no expert but I will throw my two cents in. I am the mom of a soph in college catcher who has caught since he was in LL. Those years around 15 and 16 were brutal. Lots of growing, lots of squatting.
My sons knees were sore all the time, but he never had intense pain, just ache. We have an ortho friend we would take him to who was kind enough to have him come in at 7 am before the appointments of the day to xray, make sure he was doing okay. We did this three times during those two years. I remember that about this time in the season, we had gone in because it was really getting bad. Xrays concluded that everything was okay, as far as an xray could tell. Doc told my son that every 15 year old catcher in the state was feeling the same way because of the time of season, the way 15 year old boys grow, and the amount of use and abuse the joints were taking.
His suggestion was to stretch well, ice after every single practice or game (one big bag for each knee, whether he felt he needed it or not), and if he had intense pain, see him immediately. He taught him where on his knee he would feel major things like tears to his ligaments.
Now that he is 20, his legs are like tree trunks and they are huge because of the weight lifting he has been able to do (with help of a team trainer) and he has absolutely no knee ache or pain. He's finally grown into the position!
So although I don't know about the specific stretching, I do know that the icing is terrific.
I know that time will bring more mature joints and muscles. He should lift in the off season, but use a plan that someone qualified gives him, not just go to a gym and start whacking away at it. If you live on a farm, lifting hay bales is also effective!!!
Eating a well-balanced diet that promotes growth and development is important. Recovery after practice (CHOCOLATE MILK) is very very important to muscle recovery and performance the next time you play.
If you are on a travel team this summer, make sure there are two catchers so they can split time or at least share it.
Watch your technique, if it hurts, or looks like it should, change how you squat. Knees in and feet splayed out does not look natural to me. Learn to block effectively without doing that. Get and watch Bob Bennett's catching videos (former Fresno State coach - my son had the priviledge of learning form him as he was the grandpa of our hs coach).
Make friends with an orthopedic!
Learn to play another position - give yourself an out and a break.
Being a catcher hurts. That's why they are the natural team leader, few will put on the gear. I used to tell my son to stay away from kids swingin' bats - and look where he landed. He's had plenty of collisions at the plate - your son needs to learn to handle them effecitvely too.
Learn to tell the difference in being sore and injured. Getting checked out by an orthopedic a few times when you are worried will help with this.
Have fun!