My subwoofer makes a single deep pop sound whenever i change between tuner and cd. It's been doing this for as long as i can remember. I've never bothered finding out why cuz it still pumps like normal. But today I hooked up a pair of 6x9's and the the pop comes out of the speakers too.. And there's that all too common whine as well.

Anybody have any ideas why its doing this?

The RCA's are running along the passenger side, and Power running along the driver side.
Grounding for the amp is under the rear seats so its very close to the amp.

Amp is Clarion VNET 4150 (150x4RMS)
Sub is Clarion (dont know much bout it)
Speakers are Pioneer
Deck is Pioneer.

Help!