car audio troubleshooting

soo im trying to get the best sound from my car audio. i have a set up that sounds great with cd's, but when i use my ipod through an aux cable on certain albums i get my back speakers clicking or vibrating. The quality of the downloads that i have are most likely to blame, but I cant identify the problem because each file seems to be a decent enough size data wise, anyone know what i can do?

turn the volume on the ipod down & any EQ

Absolutely turn any eq off on the iPod.

Though with an aux cable in a car I usually have to max out the volume on the iPod to get it close to line level, otherwise the noise floor is gigantic.