It will work out..... A popular saying that has become my pet peeve is, "It is what it is"..... No, it is what you make it. So is you want to be sour and complain about your situation, that is what you will get. If you want to be positive and energetic about your situation, then good things will happen.
So many variables in your story to give specific advice. He is one example. I have run 4 teams at a high school. Our best two teams were the varsity and jv. The freshmen played on a team and if you did not fit into one of these categories, you were on the other team. Your coach may be some version of this.
Be glad they are trying to run as many teams as possible. I know that almost every year I have a player that most would have cut as a freshman that ends up as a player on the varsity by the time he is a sr.
Crap even I fit that group. I enter HS as a gangly uncoordinated 9th grader and graduated as a 6'2 sr throwing 90+.