The only time i completely bypass is if the person asks for it, or if the factory amp is blown, or if im doing a full system(2 or 3 amps, 2 or 3 way components etc) where the factory amp does alot of EQ'ing that i dont wanna use so ill either catch the low level signal before the factory amp and use a intregration module like a audison bitone, jl clean sweep or rockford 360.2 to clean up the signal then get everything dialed in then shoot a flat signal to the amps and eq from there.