I am guessing it's in the flex-config.xml file or maybe the project specific project-config.xml file?
Either of those options would work, with the flex-config.xml file being entirely global.
Also, do I need to manually copy over classes I have used from my library into my project folder in order to share the project with other developers or is there an automated way of exporting the source files in this way?
For sharing source I recommend that you use a versioning/source control system (ie subversion). Then check working copies of it out into a library directory on each development machine, or, preferably into each project (as the library should be developed separately this will allow you to keep the project tied to specific revision if need be).
Alternatively you could look into distributing your library to other developers as a swc.
Cheers, Simon