Just put an eq with an aux input in the glove box and fuggedaboutit. put some velcro on the back of your ipod and somwhere on the dash and be done with it. Keep everything visible bone stock and have new speakers, self amped sub, amp, eq all new. It works just fine, sounds great and nobody is the the wisah.
Just be sure the amp drives all the speakers, and none get driven by the headunit, and the eq/aux input ipod will work excellently. If not, then the ipod will play out only from the speakers hooked thru it if you wire up half and half.
I got a shuffle for xmas and frankly it's a relief to only be carrying 185 songs...keeps picky co-pilots from scroll bitching