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So where ever the head is when you power on or reset the ardiuno is your 0,0,0. If you move the head by hand it is still at 0,0,0. If you move it with repetier or the LCD it will go back to 0,0,0 unless you reset or power cycle it (or issue some commands).
Your home and origin can be different. I stay away from that in any of my writings because it can confuse some people, and yes it is set in your CAM software. Large machines have those extreme stops so the machine does not tear itself apart. This machine has been designed not to tear itself apart, except the people that insist on using nema 23’s. The only thing you lose out on is being able to hit a “home” button. It is easy enough to just go back to 0,0,0 instead of hitting a button.
Did that answer your question.
My opinion about the whole thing is end stops add difficulty to the whole entire process (until you get advanced enough to do tool changes).
-With an end stop you need to precisely align your piece that is going to be clamped to the table to switches mounted on your machine, then make sure your origin is correct, usually with an edge finder (then you need to account for the offset of that as well).
-Without the switches, you just clamp down your work piece (make sure it is square, if that matters, usually not). Move the head to where you want it to start and hit go.