Sometimes it is obvious: "The book is ON the table." "The key is IN the bedroom." Sometimes it is not - in fact, it doesn't make sense. "I'm getting ON the airplane now" - Actually it should be "I'm getting IN the airplane." Actually riding ON the airplane would be a good trick and more than a little dangerous. I bet ON a game. Why "on"? No reason. I could logically bet "with" a game. It is just the unwritten standards that go with a language. So in answer to your question, about 80% of the time, the decision to use "on" or "in" is obvious. The other 20% of the time, it is just being familiar with English and that only comes with practice and time. One more idiom for you - If I know a secret, we would say that I am "in on" the secret. This one uses both of them.

As Maxey has explained so well, the choice is often idiomatic. Normally, think of "in" associated with an enclosed space, like a classroom. Think of "on" as residing atop something. Of course, the exceptions are too numerous to list. Don't blame me! I'm just the messenger.