For a while we were holding weekly EMAN2 programming discussion sessions, and some of these are archived on YouTube. Here is one to get you started:
These mini-tutorials are at the Python level for programmers and advanced users. They don't get updated as frequently as the normal user tutorials, so please feel free to ask questions if something is broken. They should at least give a general feel for how EMAN2 works at the Python level.
If you'd like to see something here which is missing, please just ask (sludtke@bcm.edu)!