Iv'e got a positive cable from battery to cap and a negative cable from batter to cap.
and left the amps the way they were, battery to amp, amp grounded to the body.
Essentially it works out to be the same as what your saying... shouldn't matter whether you get the power for the amp from the cap or the battery, its all the same wire.
Im an ameture though so get a 2nd opinion...
on the same topic, does the cap help save the battery from going dead that much?? I got it to stop my lights from dimming when the sub thumped.