Very well said Coach May and I agree completely.
BOF I guess what I'm getting at is the head coach is wrong if he doesn't know what's going on with his JV team. That is his future and he better know what's going on. My JV team practiced with my varsity players unless there was a game going on. I wanted to see what my younger guys had, how they handled practicing with older guys and ensure they were getting taught the way I wanted them to. It's not that I didn't trust my JV coach - in fact he was one of the biggest reasons we started turning it around. He stressed teaching / developing over winning because he and I were on the same page.
Now if your JV coach is ignoring the varsity coach because he wants to win then he's wrong. He needs to understand his role in the whole situation and accept it.
As for possible parent problems because you got their kid playing "out of position" a coach has to be pre-emptive. Sit the kid down and tell them where you see them playing as a varsity player. This way the kid can sit down with the parent and explain what's going on. If the parents still don't like / understand then that's their problem. My last couple of years at my last school I had this kid as a 7th and then as an 8th grader. He was playing first base and I knew he would be a great varsity player.....but not at first base. After his 7th grade year I told him I wanted to start working in CF and he was a natural. His parents weren't upset but they never considered him as an OF because he always played 1B. My last year was his Sophomore year and he was my full time everyday starting CF at the varsity level. He called me last week and said he just singed a scholarship with a very good JUCO in the area.
If I had kept him at 1B we would have won a lot of games but there was this other kid who could hit but probably couldn't play anywhere else. We moved the athletic kid and they both grew and developed. Now they both made a ton of mistakes early on but it's to be expected - they were both learning. One has a scholarship and the other is a valuable member of the varsity team although his sport turned out to be football.