I am wondering how would I include various elements (header, footer, nav), in one php file to be included on various pages, rather than creating multiple php files to be called
It sounds like you are trying to avoid templates. The basic idea is to define a separate file for each of head, footer, nav and include those from your content template.
...
page1 page2 page3
And to create a complete page, you would do:
Now, if I understand correctly, you want to include only one file and be able to generate the various elements (head, nav, whathaveyou). You could do this by wrapping the include statements in functions:
An article about prune juice. foobar moo
..then in your final page, call these functions: