Im gonna have to agree with mind_nl's original post on this one.. From the looks of the system you posted, you only need about a 1.5-2farad cap. A 10 is extreme overkill. And you generally do not need to use caps for your mids/highs. Just stick the cap on your sub amp, as that is what will draw the most power from your ride.
...But since you do have 10farad, may as well go ahead and use it for everything...and maybe add some LCD screens, DVD player, PS2,a few more subs, and youll still prob have some room to work with..
As for your question about alt noise, that generally comes from RCA's, or speaker wires being run too closely to power wires.