What programs/software can be run with NEA?
NEA will come equipped with Repetier firmware and host software out of the box, however NEA is compatible with all open source firmware/software bundles as well.
What would be your recommendation for a program to design STL files from scratch?
Is there a good free one and one that is not too expensive?
If you are looking to explore different programs we can recommend;
Free: Sketch Up, Blender, Tinkercad, Autodesk 123D.
Commercial: 3D Studio Max, Autocad, Zbrush, Solidworks