CNC Positioning

Hi

Please don't $#@$ me for the stupid question I am going to ask now!!!!

I want to try my hand at building a CNC router. Got all the parts etc.

I would just like to know how do you tell the router where to start
the cut? Say for instance I have an irregular shape mounted to the
table, do I zero the controller or at the software???? Especially
after say changing cutters or routing on both sides of the object.

Sorry, extreme stupid, but never seen one of these in action, just
dreaming of trying my hand it.

Your answers will be greatly appreciated.

Regards
Ruan