Alright, I'll try my best to explain these basics:

- The things you are referring to are the actual folders in the file system that make up parts of concrete5. You'll only see these folders if you look directly at your webserver's files. For the majority of editing tasks, you don't have to concern yourself with these folders and you won't seem them referenced from within concrete5's dashboard/interface. Some CMS will directly show files and folders of the file system in an admin - concrete5 doesn't do that.

- In fact, don't EVER edit anything within the /concrete folder. This is the 'core' folder and holds all the files that makes concrete5 run. When concrete5 is upgraded a version, it's this folder that effectively gets replaced, hence why you never want to make changes to it directly - they'll get overridden in an update (or you might break something).

- Also, for all intensive purposes you shouldn't edit anything in the /files directory. This is where uploaded files are stored, but you don't ever upload files to these folder directly, instead you use concrete5's file manager to upload and manage files. Just let it do it's thing.

- Any of the themes found in /concrete/themes are the base included themes, where if you looked you'd see template and css files, but again you don't directly edit these themes (because it's in /concrete). If you want to make visual changes, the built in themes and many from the marketplace allow you to customise them safely via the dashboard, see: http://www.concrete5.org/documentation/using-concrete5/dashboard/pa...

- You will see through the forums cases where people talk about adding files to top level directories. In these cases it is where people are wanting to 'override' existing concrete5 functionality or output. If you do look at the folder structure you'll see a bunch of top level folders where most of them are empty. The idea is that if there is something you want to adjust, you can drop copies of files into these top level directories and they'll override the core files. This means you can upgrade concrete5 without losing any customisations. http://www.concrete5.org/documentation/introduction/overrides...
It's only if you've exhausted your options using the actual editing interface of concrete5 that you'd look to putting in overrides. In other words, this is for developers, not site editors.

- The most common 'beginner' reasons why you might start looking at the actual folders of concrete5 are when you are either wanting to build your own theme (so you'd put something in the /themes or /packages directory), or you are wanting to override the output for a block. For example, you might use the Page List block to output a list of pages, but you might want to tweak the way the HTML is output - in this case you can create a template for the block and put that in the top level /blocks folder. Then you can select your custom template for the block, allowing you to create a custom output. Between creating a custom themes and creating custom block templates, you can basically control the entire HTML output of concrete5! There are lots of how-tos and guides in the doco on how to do both.

- Let me stress though, the folders you are mentioned AREN'T intended to be edited by complete beginners, hence why they're not really mentioned in the beginner documentation. Complete beginners should be installing concrete5 and building their site via concrete5's editing interface. New themes and add-ons can be installed via the marketplace and that takes care of putting the files and folders in place. It's only when you are wanting to start to customise your site further that you'd consider these folders.