The biggest offender of noise in the car audio environment is alternator whine. Alternator whine is caused by a difference in electrical potential (voltage) between two points. It's usually caused by a ground connection that is less than ideal. The main culprits are the amp, the head unit and any intermediate components such as crossovers and equalizers. Basically any component that touches the low level music signal (from RCA cables). It's usually cured by finding the source of the noise entrance and re-grounding that component.
You can usually isolate the head unit as the problem by disconnecting the RCA cables from the amplifier and inserting a muting plug (RCA plug with the connectors shorted together). This also eliminates any noise from components upstream of the amplifier such as crossovers and equalizers. If the noise is gone then you need to check the other components upstream of the amp. First, connect the head unit RCA cables directly to the amplifier (assuming you have crossovers or equalizers between the two). Start the engine. If the noise is gone then your problem is the intermediate components. If the noise returns then it is a head unit problem.
In almost every case you will simply need to find a better ground location for that component. Clean, bare chassis metal is the best solution. Many times installers will use whatever factory bolt is handy and that can work but it can also cause problems. Factory bolts are not a bad source necessarily, but if they have other electrical components using them as a ground this can be a source of noise. If you're not using a new ground point then you'll want to make sure your factory bolt meets the criteria above.
The next step isn't as much fun but it's needed to know for sure. Remove the deck from its mounting location and place it on top of the amplifier. Put a non-conductive barrier between the two (a folded towel is fine). Hook up the deck's power leads (power and ground) to the amplifier's power terminals. Then connect the head unit to the amplifier with very short RCA cables. Male to male RCA gender changers are about the right length. Start the engine. If there is still noise then it's a rare head unit problem. Most likely it's coming in on the cables. A switch to unshielded, twisted pair RCA cables can help that if the noise is being induced along the cable run. Also check for open RCA shield grounds on your head unit as this can be a source of noise. Other times you will need to run the head unit's ground wire to the same grounding location as the amplifier. I'd recommend using 16 gauge wire for most longer runs (10-20ft).
OK, there is a third thing you can try. If neither of those solutions work for you then a ground loop isolator can be used on the RCA cables. This is basically a small box with 1:1 transformers inside. It decouples (breaks) the electrical connection of the RCA cables and replaces it with a magnetic coupling. This eliminates the noise since the music signal on the RCA cables is AC voltage and the noise is DC voltage which cannot pass through a transformer. Depending on the quality of the isolator you can lose some signal quality so this is not a good solution if extreme fidelity is required.
You may also be interested in How to Install Your Own Car Stereo System . It covers many topics including in depth car audio amplifier installation. Click here.