I have a a module that I want to include in the swf build but I want the swf to be able to use the module (separate swf) externally. How can I build both the application and the module in different swf files? (I know it's something with the compiler, but not quite sure)
I'm not really sure what you're asking, but here's how to tell FlashBuilder that you want a module to be built:
Right click on the Flash Project, select "Properties", then select "Flex Modules". Click "Add", and you should be able to browse to your module.