Well I have finally decided after much testing to use PHPDocumentor to document my source code. I am moving into PHP from Java, so I am familiar with JavaDoc style comments. I wanted to be able to continue this in my PHP source...PHPDoc (the one that actually uses JavaDoc) seemed to have issues building the package structures...So I opted for the PHP driven PHPDocumentor.
I have been busy editing all my source files to bring them up to speed with the features of PHPDocumentor. And soon an online API for my source will be available at the projects home page. http://phpwebengine.sourceforge.net
This home page is another issue I am working. I am good at PHP and server side scripts...HTML and graphic design are not really my thing.