One nice side benefit of the fact that we use Eclipse as the host for Flex Builder is that it means that within a single IDE, you can simultaneously debug your client-side Flex code and your server-side Java code.
Eclipse allows you to have several debugging sessions going at the same time. So the “Debug” view can have, for example, a Java callstack showing the code in your server app, and a Flex callstack showing the code in your client-side app.
To do this, you will need to be running the “plugin” version of Flex Builder – the version that runs as a set of plugins on top of a pre-existing Eclipse installation – rather than the “standalone” version.
Last month, James Ward did a thorough write-up on how to get this working.