The process of linking your side nav and content area is a manual one. You would need to create and maintain the side nav separately from the main content. On each page you will have the code for the side nav and the code for that pages content. You will need to make sure that you page names match the links in your side nav.
When you go to your domain without specifying a page it will show your default document. I usually make an index.php page for this. This is the page that will be displayed by default when a user visits your site.