Well if you really want to do it the hard way , then simply use a text editor and follow through the Glassfish tutorials.
But seriously you can use an IDE and still get a good understanding of the basics, just make sure you investigate XML configuration as well as Annotations and you should get a pretty good 'manual' picture of what is going on.
I personally learned off the OReilly Enterprise JavaBeans (5th Edition) book which comes with a large tutorial section that takes you through the basics of EJBs using Jboss. Much of the tutorial is stand alone as opposed to servlet driven so you gain an excellent understanding of the basics.