You seem to have a couple of problems. There is a very simple solution to fix all of your problems. Leave all of your headunits wires hooked up except the speaker wires. Go purchase new speaker wire either 16 or 18 guage wire if you are not using any aftermarket amps and run new wire to every speaker. It is not as hard as it may seem. The new speaker wire will be labeled which side is pos. and neg. Match it up to your speakers pos. to pos. and neg. to neg and then to your head unit. To avoid getting confused run one set of wire at a time. Example front left speaker and wire to the front left speaker wire comming out of your headunit. Then do it again 3 more times to the left rear, right front and right rear. Now you know that your speakers are in phase, your fader front to back works and your balance left to right works. This is the best method to get the most out of your headunit and new speakers.
If you have anymore questions pm me or shoot me an email. ENJOY