I use FlashDevelop for Actionscripting and sometimes I need to export multiple SWFs from a single project. You just need to use the mxmlc compiler tags in your AS class file (make sure the class extends a displayObject) and use Flash Tools > Build Current File.

Here is an example of the mxmlc with a bunch of settings that are fairly self-explanatory. For multiple SWC files just define the -l lib tag again. To see a list of all the tags use the @mxmlc -help tag.

[code]
/**
* @mxmlc -help
* @mxmlc -o bin/create_banner.swf -debug=true -default-size 1024 768 -default-background-color 0x000000 -use-network=false -l lib/login_all.swc -l lib/customFont.swc -l lib/CreateABannerAssets.swc -l lib/aether.swc -source-path=Z:\AS3_classes\
*/
[/code]