If all you are doing is changing the speakers to an aftermarket type, all you have to do is cut off the terminal ends from the speaker wiring harness and solder these wires to the speaker terminals on the replacement speakers. If you do that, make sure that you use the correct polarity, otherwise they'll be out of phase and the sound will suffer.
Read this to give you an idea of what I mean: http://www.sfxaudio.com/AudioSchool/installspkr.asp