There’s a really cool article about the embedding of resources in Actionscript 3 in Keith Peters bit-101 blog.
If you’re using his technique you can get rid of that awkward Flash GUI and just develop Flash applications with Eclipse in combination with the Flex Builder plugin by Adobe (currently you can obtain a free license for the Flex Builder Plugin as a student) or with the FDT plugin by Powerflasher.
In the beginning you need the Flash GUI to put all the graphical stuff you need in the library of one Flash file each as a MovieClip symbol. Afterwards you export the swf, put it in you main source folder and follow Keith’s instructions.
I use this to embed Vector graphics I get in an Illustrator format from a Designer to embed it as a Vector graphics in Actionscript 3.