On the Geekzguru.net site there's a guide posted (from June 13th) about how to get PDT and Flash Builder to let you debug both sides of your application (the Flex side and PHP side) at the same time.

This setup allows you to edit and debug you PHP files along with your flex application in the same instance of eclipse. All features of PDT like PHP code coloring, auto complete will be available in addition to the wonderful features that Flash Builder 4 provides.

They walk you through the installation of the Eclipse PDT software, the XDebug module for debugging your PHP and how to modify your Flex project's files to modify the .project file's XML with a new linked resource.