PHP4 Output

In PHP3 I could run a PHP program by specifying a filename as a parameter. I realize that this feature is still there in PHP4 but I think the way it works must have changed. It must also be able to get the file to run from somewhere else. I call PHP directly from a different CGI script. With PHP3, I could make PHP run on different files from within the original CGI Script. Now, no matter what filename I specify as a parameter, PHP4 is going to run on the same file that the original script was called on. So, my question is, how do I make this work in PHP4? What other way does the PHP exe get the file it is parsing? Can I just change a environment variable or is it more complicated than that? Example: My original file is a Java program called on main.html. The java program then calls PHP twice within itself to add a header and a footer that is common to my other PHP files. The old output was main.html with the header and footer added correctly. Now, the browser receives main.html with it inserted into itself twice where the header/footer should have been. This is causing a major problem. I would appreciate any help on this subject. jordan