That's a tough one! Now without more detail, it's hard to say. There are reasons why things are done the way they are, but there could be a better way of doing things.
I've had that happen, and I always tell the person to do things per company policy or procedure, then we can see how to improve that process. But you need to learn the prescribed way before we move outside of that box. Don't stifle that objective to look for a different way, but reinforce we can't look at that until the set process is followed. Then have the employee "show their work" to demonstrate they learn that process, then talk about how that process can be improved.