I am currently running a Kenwood Z727 head unit with infinity kappas (green ones) all the way around and I have a four channel amp ready to connect (wires and power already roughed in). My question is...when I hook up the amp using the pre-amp outputs do I need to disconnect the speakers at the head unit or just at the doors when I connect my new speaker wire from the amp?

 

It would be a good idea to disconnect the speaker wires from the HU, but is not absolutely necessary. If you were to just disconnect at the door location, there is a possibility that the wiring could short (get pinched by the window or something?) and might cause a problem with the HUs internal amplification.

I have decided that it is much better to spend a little extra time and make your system as robust as possible in the beginning, than it is to have to repair something later!

Have fun with your system,
Rob