Let me tell you something about QCMS lite, the Content Management Software used for this website.
The file structure looks like this:
all the blog entries go in here
stylesheets go in here
cascading style sheet for the template
all images files are stored here
all important php includes go in here
all the pages accessible in markdown format go in here
the default 404 page in markdown
all the site modules go in here
generates a menu with all files in the same level
all the pages accessible in php format go in here
the blog page which is used as startpage on this site
rewriterule for domains
this is the core of QCMS
Whenever I need to add a page, I simply create a text file and put it in the markdown directory. It will be automatically added to the menu. For new blog entries, I simply drop the text file in the blog directory. It will get ordered correctly and displayed on the main page.