That doesn't actually answer my question at all.
You seem to be getting very confused about the scope of your project and/or tools. Eagle is an electronics CAD tool, for designing electronic hardware. Your hardware may contain an Arduino in one form or another, or it could be a module to plug into one. For this, you need the hardware details of the Arduino in question - the pin-out and electrical specs. You also need some idea of what your circuit is going to do with the Arduino's pins - what sort of analogue sensors you're connecting and what actuators you're driving.
Notice that at no point in the above did I say anything about "program" or "hex files" or even "microcontroller tasks". That's because the whole essence of a microcontroller is to remove the actual functional detail from the electronic circuit design, and instead to encapsulate it in a "program", which is developed independently and almost always well after all the electronics has been finalised and built. You use a completely different tool chain for that part of the project.
