To be honest, if you ready to design your own board, you shouldn't need to ask these questions. But I don't have the Mega schematic with me since I am on my tablet. I will get back here tomorrow with the answers.On a side note most of those are statements, not questions.
CADSOFT EAGLE or Altium Designer
Both have free versions.
there is fritzing and PCBWEB , 123d.circuits.io , EasyEDA
my designs are too complex for that.