Flex Builder is delivered in two flavors: one is the standalone version and one is a plug-in version for Eclipse. Because I want to be able to use the same IDE for editing both PHP and Flex code in the same project, I need to have Eclipse with both Zend Studio and Flex Builder installed.
The easy way to do this is to install the Zend Studio for Eclipse first, and then start the Flex Builder Eclipse Plug-in installer. Make sure you choose to install in the Zend Studio Toolbar (this will help you to debug the PHP code). At some point, the Flex Builder 3 installer will ask you for the location of the Eclipse installation folder to which you want to add Flex Builder (see Figure 1). You can use Zend Studio 6.0, 6.0.1 or 6.1 (which was the latest when this article was wrote).
After the installation is done, you are ready to use these tools on Flex and PHP projects.

Figure 1. Selecting the Zend Studio installation folder