Overall design strategy.

I’ve gotten to the point where I’m fairly comfortable with lwjgl, however; my issue is that when I start a new project, I have issues deciding where to put everything in the overall structure.

ie: I don’t know where to put certain rendering methods to make everything easier on myself.

Are there any design structure articles or references that might be of use to me?

or do you guys have any suggestions on how to plan out the structure of the game?