From the sound of the question you are looking for a simple overview to help you get started. I would suggest that rather than initially tracing the way that the (labyrinthian) drupal core passes requests through functions, you should start with looking at how simple modules and themes connect to it to get an idea of the larger design pattern. Once you have an idea of the concepts and terminology used, the commented code examples are invaluable for this, giving examples of things you can do, and describing how to accomplish it.
Basically, as Djouuuuh points out, you can safely leave drupal core to do its thing. That is why you will work exclusively within the sites directory. Your interaction as a developer is to configure the installation to behave how you you would like (site building), create themes to customise display (theming) and create modules (development) to match very site-specific functionality. Always look to existing, supported modules first, it will save you a lot of time, even if must add to their functionality with your own module.
To understand the naming conventions for files and functions used in modules and themes, you will need to learn about the hook system and then look to the examples and the API(via google) to understand the uses of those hooks. More than likely you will rely heavily on just a few hooks to start with, for example hook_menu, hook_node_load, hook_form_alter (forms are a big subject).
Drupal.org holds extensive documentation about development methods.
Also Jeff Eaton of lullabot looks to have created a good slideshow on the subject of drupal development, which might be worth a click through.