alternator noise in subwoofer?

I have been hearing a low noise that sounds like my exhaust that is louder than usual.  I thought I had a hole in my muffler or something but I realized it was my subwoofer making the noise when I shut my HU off one day and it stops.  It gets drowned out by the music above minimal volume, but it when the car is idling and the volume is down it is apparent.  The noise gets louder if i tap the throttle and rises and falls with the RPMs. 

My setup is as follows:

Pioneer DEH-P840MP

I cant remeber what type of cables I used.

You have a blown surface mount fuse on the circuit board of the radio.  This fuse protects your radio in case a 12 volt wire touches the shield of your RCA cable.  The simple fix is to solder a wire to the outer part of one of the RCA cables that go to the sub amp and ground the other end of that wire.   The yellow wire in the following link really needs to be a black wire and you need to ground it to wherever you grounded your radio.

Thanks for the reply.  I cannot view your link.  Could you check to see if it works for you?

I have heard of the method for grounding the RCA shield, but am wondering why if there is a blown fuse can I not just replace it?  I dont mind taking my HU apart I have already had to do it once when the motorized face ribbon cable wore out (a common problem with my HU - it has happened to me twice in 5 years...but thats another story).  Where in the HU would I find the fuse, and is it worth it to replace it?  what blew it in the first place?

You can replace the fuse if you want to.  It is a surface mount device.  You will need to take the radio apart and notice where the Shield of the rca cable or jack meets the circuit board, and follow  that trace to the first component in it's path.  Using a meter check to make sure the other side of the device is connected to ground.  So basically if one side is connected to the shield of the RCA cable or jack and the other side of the device is connected to ground then that is the blown fuse.    what blew the fuse is one of 2 possibilities that I know of.  1  the shield of the patch cord came in contact with a 12 volt wire.    2   You either had a ground wire of your amp came loose and the amp was trying to find ground via the patch cord.   Or when installing your amp you connected the RCA cable and the power wire before you connected the ground wire.  Once again the amp had power and no ground and tried grounding via the RCA cable.

OK well I figured out an easy way to solve the problem - but i still have a question.  The noise was apparently only coming from one of the two RCA cables.  One of the cables when connected (to either amp input) produces ONLY the noise.  The other cable (when connected to either amp input) produces clean bass with no noise present.

My question is (and I never understood this to begin with) - why are there two RCA output cables from the HU anyway?  Are they redundant?  Do they produce the same signal?  A subwoofer should only need one channel of audio right?  So thats only one RCA cable.  Can someone clarify?

There are 2 sets so you can have a front and rear output.  So you can fade front to back.   If you had a mono sub amp and a mono sub out on the deck then yes you would need only one output.  Just in case you have a 2 channel amp bridged on your sub, they want you to be able to feed both channels of the amp.   

Cold solder joint or effects of compressing a picture so it will post here?