Isolate each component in the system is not a source for noise to enter, or the cause of a noise.
The Shorting Plug: This is used to check individual components in the system. To make a shorting plug (you will probably need several) you will need several inexpensive RCA cables that can be donated. Cut all of the ends off of the donor cables, leaving about 2” of cable on each end, and discard the remaining co-ax. Strip the insulation from the outer conductor (shield or ground) and fold the wire aside, and then strip the insulation from the center conductor. Twist the shield and center conductors together, then solder and insulate with tape or heat shrink. Do not connect multiple plugs together.
Using the Shorting Plug: When inserted into the RCA inputs of a component, the inputs will be shorted (no damage will result). Do this one component at a time, starting with the amplifier(s), leaving the speakers connected. Once you have inserted a shorting plug into all RCA inputs of a single component, crank the car, turn on the system and listen.
If the noise is gone, move on to the next component and repeat the process.
If the noise remains, check to see if the component is mounted to the chassis (metal) of the vehicle. If it is, see #5 under Noise sources / Points of Entry.
If the component is not mounted to metal and the noise remains, then run a new power and ground wire outside the vehicle. If this eliminates the noise, then the noise is getting into the system through the power and/or ground connections of the one of the components in the system. This will require finding an alternate path to the battery, and possibly another point at which to ground the system components. Carefully observe the path your power and ground cables take through the vehicle. If they run along side (parallel) any factory wiring, this could be the source of the noise.
If the component is not mounted to metal and the noise remains after trying an alternate route for the power and ground connections, then run a new RCA cable(s) outside the vehicle. This step can be used at any point during troubleshooting, and can be between any components in the system. The RCA between the signal source and the first component after it is the most likely candidate. Since the RCA(s) between the source unit and next component tend to be the longest, noise can enter anywhere along this long connection. Carefully observe the path your RCA cables take through the vehicle. If they run along side (parallel) any factory wiring, this could be the source of the noise.
Noise Filters: Suffice it to say that these are a gamble at best. Most ‘RCA type’ noise filters de-couple and isolate signal ground paths. In the best case, they remove the noise and nothing else. In the worst case, the noise is gone, but so is the bass, or maybe the noise got worse and the bass still went away. Use at your own risk! As far as power line filtering goes, most amps already have this built in, and adding more may or may not help. The biggest problem here is the current capability of the filter. A filter capable of the current flow demanded by say, two 1000 watt amps, would be really large and expensive. Not to mention that you would have to have it custom built!
Finally: If none of the above steps at least locate, if not reduce or eliminate the noise, then it is time to have the components tested by a qualified technician or by the manufacturer; or live with the noise.