ground isolators do not fix noise, they hide it.
Your sub has nothing to do with the noise.
Your ipod or cd creates a signal inside the headunit. The headunit sents it to your amplifier via the RCA's. The amplifier multiplies that signal to make it louder. Then the amplifier sends the signal to your speakers.
Are your power wires/remote turn-on wires on the opposite side of the car as your RCA's and speaker wires?
Power wires create a electromagnetic field around them that will cause distortion in your signal (rcas & speaker wire)
If you have to cross the wires, cross them perpendicularly (at right angles).
Check your ground wires. Make sure you sand your ground location down to bare metal. There can be no paint left on your ground location. If there is, it will cause noise in your system. Do this with all of your ground locations.
Your amplifier's gain is not a volume nob. The gain is used to match the voltage from your headunit. To do this correctly, you need a DMM (digital multimeter). A $15 one from pepboys or walmart will work fine. Look up more info on this once you get one.