once you've ID'd everything you need, tested it and you know it works, then at a minimum tape off the unused leads. better is clip and tape off if you have lots of slack and no specialized connectors you care about trying to use later.

in terms of what you need, well i assume you need at least four speakers, gnd and two power leads. do you have a sub? test to be sure that sound comes from every speaker in relatively the same loudness. i don't mean twiddle the balance, but more like, if two are active and two are passive, you may have a wrench in the works. once you are satisfied with the sound coming out all of the speakers, and it works properly, tape off and bundle the unused leads. label them if you know what they are by that point in time. depending on how many you have left, stuff them in some wire loom or at least secure with a couple cable ties so they can be stowed back behind in that tangle of crap back there.

what to do with the antenna wire? that's up to you. do you listen to AM/FM? if so, connect it. if you don't, you may turn the unit on and the antenna automagically goes up and stays up. mine did, and so i connected the antenna wire temporarily so the antenna mast went down, then cleanly clipped and wrapped the antenna motor positive in the fender.