I found this adobe help page but I didn’t want to use command line for packaging an AIR installation file. Simply because I’m not used to it. So I was looking for a different way.
Well, actually Flex Builder provides the possibility to do that, but you must ensure to activate the “Copy non-embedded files to output folder” compiler option in the project properties. Otherwise Flex Builder won’t let you select your additional sources.
And for that reason you have to put your additional sources to the src-folder.