I will have multiple folders/modules to access common files. But accessing them seems to be big deal for me!
I did gone through this link to understand the relative pos
Your PHP-includes seem to be correct. But in your HTML you need to change the linking to the CSS and JS Files (maybe even to your images).
You could use absolute paths:
the leading dot makes your paths relative to the HTML-Document, so if they are linked from a document in a subfolder, they point to a wrong location.