I sort of understand what and why people go for stand alone engine management i think thats what you call it? dta, emerald, ms, omex and so on.l

What i cannot get my thick little head around is when you piggy back these systems onto a cars normal engine management how does it know what controls what and how? The bit confuses me most is when you ditch the standard wiring to the engine; would the standard ecu go ARGH no sensors lets put on the mil light and not let the fooker start up! For arguments sake say a Focus how do you get it working assuming the new box ready set up for a zetec engine?