The dog doesn’t learn respect, you earn it!
I must say I am surprised to read your message on Robert Cabral’s site because it seems you’ve joined without actually learning anything from his extensive resources!
I suggest you stop everything you are doing with this dog because it’s already going in the wrong direction! This poor puppy is going to end up seriously hurting you or worse someone else!
A crate is NEVER USED FOR “PUNISHMENT“. It’s a safe place for your dog to chill and be left in peace until he is needed for training, exercise, play etc.
The first thing you need to learn is about resource guarding. Malinois have a habit of this type of behavior and if not addressed can lead to aggression (you’ve already got to this point) Robert has very good videos on how to deal with this behavior. Go look now!
Once you sorted out this issue. You can move on to basic training. Every puppy needs basic training and socialization. Build new skills ONLY once your puppy had accomplished the first, then revisit old skills to keep fresh and well tuned.
Keep training fun and short. You end the session not the dog. Do not repeat an instruction, it falls on deaf ears, especially with a malinois. Get your dog’s interest with a toy, ALWAYS REWARD GOOD BEHAVIOR within seconds of it being achieved. Make it fun. Your dog isn’t a slave to do your bidding in the hope suddenly it will respect you!
Respect is a two way street!
Follow Robert’s puppy classes before your poor dog has to be put down because of your own insecurities.