well it depends on the plug and play i went ahead a built my own wiring harness for the engine but i have an automatic so i left the stock computer in the car.. what i did was let the MS control the timing, fuel, and be solely hooked up to the coolant and air temp sensors as well as the idle air control...but the OEM computer and the MS both see the basic stuff like throttle position, crank position,etc so it can still tell the transmission when to shiftand work all of the gauges and lights. the megasuqirt is controlling the fuel pump relay as well.. so i have all the factory functions of the oem ecu just the megasquirt is tied in to control all of the actual engine functions..works great.. i can thank matt cramer for that idea. i emailed him about 500 times with questions, and not one time did he get upset or anything..diyautotune is the way to go they are great..