After reviewing the file structure, I have decided to remove the implementation layer and place it in the main files. All the design abstraction is in the templates, so adding another layer between the file itself and the implemented code is silly. The folder structure for code is currently:
This is were the front end files are actually located, the inline code that actually does the stuff is located here.
This is where the class and core logic files are located. These are strictly functions and classes, absolutely no inline code is allowed in these files.
Where the smarty templates are located. Smarty script files are in the core directory.