typical noise issues are caused by ground loop... your deck and your amp see fluctuating ground potentials relative to eachother and because of poor isolation between the signal ground and the power ground of both your amp and HU noise is introduced.....

by far the best solution is to use an isolated dc/dc power supply which will give your hu a floating ground which is completely isolated from your car's electrical system......

more common fixes include:
-line driver which minimizes the noise floor
-choke on deck's power ground which filters alternator whine out inductivley
-transformer on the audio signal.. transfers low level AC signal through a transformer which breaks the direct path in your RCA's needed for noise to pass (high quality transformer needed or it will mess with response and phase by inductance of the windings)
-power supply with active suppression.. takes AC noise superimposed on your DC power line and creates an identical signal 180 degrees out of phase (I think)

many amplifiers also use (pseudo)balanced inputs which work with t/p interconnects to cancel noise

 

Woah, That cleared up quite alot of things !
But Since Im not ganna plan on building a big system, It should be of a problem, but if anything comes up, then I know of my options !