I would really recommend starting with writing plugins for systems that have good structure, well commented code, stable development, etc. You're going to be learning a lot from the code you're working with, and it's a lot better to learn good habits and then adapt to working with a horrible code base like OSCommerce than the other way around.
But to answer your original question, there's really only so many ways to to structure an application with slight variations, so once you start working with a lot of different systems and get comfortable with them, picking up a new one and understanding it isn't an issue.