I’m not quite sure what that means or how to implement it. Does the index.php contain a script that loads in content, based on what url the user is viewing? If so what would such a script look like?
Before coding anything, think through what those 400 pages have in common. The point of a single point of entry is not that it is good in itself, but that you are trying to separate content / data from how it is presented. For example, a blog site might have 400 posts, but each post would be essentially the same. They each have a title, a date, an author, and some content.
An important first question – have you used databases before and are you currently using one?