In the Project Properties -> Main Module, I think a bit of work needs to be done on the whole concept of Libraries.
It was at least partially intuitive in previous versions of IntelliJ IDEA, but in the EAP, it's very confusing and counter-intuitive, IMHO.
Is work already planned on improving this before 4.0's release? Or is the current state as good as it's gonna get? I will enter a feature request if appropriate.
Quickly, a few issues:
1) Can't edit a library unless you go into the "Add" button. Should be able to edit directly from the main window.
2) Add Global|Project Library should be moved into Libraries tab. (I've actually already entered a feature request on this, but it's not open. http://www.intellij.net/tracker/idea/viewSCR?publicId=19861 )
3) What is the points of the Named Library in the Libraries tab if you've got Project and Global Libraries in the Order tab?? This is so confusing!