There is no "right" way to do things without knowing what "things" are. MVC is a design pattern that solves a specific common problem - separation of presentational and domain logic. Every design pattern is a commonly accepted "good" solution to a specific problem.
Those solutions, combined with knowledge and experience are building blocks for a good design. The "right" way to do things is to study your problem domain, research on possible solutions and apply the set of solutions that work best to solve it. Making mistakes is a part of the process as well, so don't be afraid to experiment and then refactor with rigor until you reach the solution that serves you best.
