I'm not sure what the exact problem is with your packages but let me tell you how mine works. First of I'm using an IDE (eclipse to be exact).
When creating my packages I make sure I have a main package (which is the name of the game) and then the sub package. For example:
Every single class that has anything to do with entities will be put in the entities package.
the hierarchy of the files should be something like:
As for other tips you might want to use 2D libraries like lwjgl or slick2D (which is a "fork" or not sure how its called from lwjgl). Oh and i suppose you could find some great tutorials on youtube (instead of plain text websites).
If you use lwjgl check this link. He has some amazing tutorials.