Bypass the factory amp or stick with it?

[xdviper]

I've installed a new head-unit on my 97, without the JBL audio system but with the AUTO button on the factory unit. This meant I have to bypass the amp that is the rear of the vechicle. I connected the new JVC headunit via the harness that connects to the factory amp and distrubutes sound that way.
Now the problem is, just a few days ago, the left side has been going in and out. When I turn up the volume, the left will start working again, let it go down, it'll be mute. I've taken off the door panels and checked the wires and everything is firm. I'm also using 4 aftermarket speakers that worked before and after I installed the new headunit.
I've troubleshooted my way down to the amp being the culprit. I have the amp bypass harness (a bunch of long wires) and haven't installed it yet since it was working fine. But want to get a few ideas or tricks before I go ahead with the bypass.
Would the amp be responsible for the left side going in and out?
And how would one bypass the amp? Where do I run the wires from? And how? Under the carpet? Can this be tackled by someone who has no experience taking apart a whole car?
I know I can run the wires from behind the head unit to the glove compartment and then what? Thanks!

 

[Anime]

Since you already have an aftermarket head unit, and aftermarket speakers, you could just use the head unit to power the speakers.

You can buy a bypass wiring adapter to use the factory wiring, or just buy new speaker wire, and run the new wires from the back of the head unit to the speakers.

You can run the new wires under the carpet and under trim panels, all you'd really need is a screwdriver to remove the screws, and you can just snake the wire through hard to get to areas with a coathanger or something.

 

[Crutchfield Vlad]

Since you have a new Headunit, it's more than likely it's the amplifier. Using a Harness like this, you would run it from from HU through the glove box then down under the bottom door panel and back to the amp. You could just use a panel tool to pop of the panels to hide the wire. That harness will connect the HU to the output of the factory amp, so you will still use the existing wires from the amp to the speakers.
Other option would be to run a new speaker wire from the radio directly through the door hinge and connect the speakers. That's a little more difficult cause you are re-wiring each speaker but it would be better since you would be using less wire (more direct flow=better sound) and the peace of mind that it's done right without any breaks and/or wire splices.
Both options are doable for first time do-it-yourself but running the speaker wire directly will take more time cause you are taking apart more panels.