If you have a complex project it might be worth creating an ant build task. This lets you have very specific control over the build process and parameters.
You can download ant from the website (manual here) . There is a version that's included with eclipse, but I prefer to run it through the command lines.
Flex builder comes with an ant library that defines tasks to build actionscript and mxml files. There's some documentation here
For instance, this is a sample mxmlc task that you can do by running 'ant production-compile' :
<target name="production-compile">
<mxmlc file="myApp.mxml"
show-actionscript-warnings="false"
output="myApp.swf"
debug="false"
optimize="true"
>
<default-size width="800" height="600"/>
<default-frame-rate>60</default-frame-rate>
</mxmlc>
</target>
You can add mxmlc tasks for each of your modules, and this will let you build the whole application with one command.