It sounds like you've wired your rear speakers to your deck's front speaker output.
I had a few similar issues until I found out that the speaker wires in my car swapped colour half way down the car!

It may feel like all yours speakers are 'connected together' as more than likely, your rears are connected to the front output, and your fronts are connected to the deck's front pre-out - so fading to rear would lower overall volume.

Take the head unit out and and connect one speaker at a time while testing balance and fader making sure it is the right speaker that's connected. (only the speakers running directly from your deck, amplified speakers seem to be properly connected)

Good luck mate.