I know it's engine noise (that's the sound anyway) but it seems to be the loudest in one speaker, the right rear 6X9. I have heard it before but it is much worse now, how do I get rid of it. It's to the point where it's a loud whine with a crackling sound to it as well.

it could be near a power wire some times that makes them get engine noise

Crackling sound usually equals blown speaker. A power wire near the speaker really wouldn't cause whine. Now a power wire near a signal wire (RCA) would. It could also be caused by a bad ground, but usually all you get is whine, no crackling.

Well crackling is not the best way to describe it I guess. It's more like when the whine starts it will be high pitched, then it starts to get deeper, and then does this static type sound. You know how static sounds crackley.... Does that help?.....lol Also it seems to be mostly out of one speaker, not the whole setup.

Bad ground???

Like said in another post, gently push on the speaker and if you hear or feel something rubbing, the speaker is bad.

That sound is more then likely going to be a standard ground loop. Ground loops usually occur when A number of components are installed in various locations in the vehicle. When the components are grounded in different places, a differential voltage is created between areas of a car.
You will need to try to consolidate as many grounds as you can into one ground point... but be practical and try to keep ground wires under 2ft long.
If that dosent work you may want to take a look at your batt. if it has been deep cycled enough times it will not properly filter current causing the alternator whine you are hearing.... Good Luck