We currently don’t support the library deployment features that you are asking about, but since library sets were introduced into Eclipse 3.0M8 we are looking into the natural addition of them into MyEclipse as well as associated enhancements (like you accurately pointed out).
As far hasving multiple source folders, sure. Open up your project properties, go to your Java Build Path node, and click on the Source tab, and add another source folder.
I will pass your request to the devs so we can keep this consideration on our radar when we do add library support.