distinguishing the wp code

Huh?
index.php is the ‘base html’, if you want to look at it that way. You can go and add custom php/html inside the menu div, or create a separate header div or something, to create links to wherever you want.
The system can also automatically create lists of links to posts by category or by date/order, etc.
That help any?
=d

From my site:
Index
About page
You can see from that how I used the index.php to make the base for my about page. You can go one step further, and make it all includes. One common include for the header (css etc.) and one for the bottom of the page (what’s past the body content). That way, you just include, and go.