OK. 1st Arduino needs to be running.
I think that the last option that you mentioned might be the one I am looking for. Do all my parameters that I want to change have to be in setup() or can they also be in loop()?
My Arduinos are not yet connected because I don't know which is the best or right way. Maybe through serial connection? Maybe with AVR programmer? No clue.
Please point me in the right direction.