You get both versions. AIR is integrated, you don't need to install anything unless you want to use the AIR 2.0 beta SDK.
The easist way to do Flex and Java development is to use the plug-in installer (instead of Standalone). The Flash Builder 4 Plug-in installer includes Eclipse 3.4.2. You can download 3.5.2 if you choose, then point the FB installer to use that 3.5.2 distribution instead of the included 3.4.2.
Jason San Jose
Software Engineer, Flash Builder