Sorry about the late reply but yeah I've used that harness before but it was a different brand on one of my previous cars. You run the bypass harness like you'd be setting up aftermarket amps/subs. The second harness is really long and you pull up the sills to run it along the side of the car under the carpet into the trunk. You then disconnect the harnesses leading to the factory amps and just plug them into the bypass harness. It's super simple. I ran mine along the passenger side then under the back seat. What it basically does is use the factory connections to run the speaker level outputs from the new head unit to the back where it would normally go to the amps and instead goes around them and connects straight to the speakers using the factory plugs from those amps to send them back up front. It jumps the input side of the amps and plugs them straight into the output plugs. You can sort of accomplish the same thing by making your own wires if you can run them the same way and crimp or splice them to the unplugged connectors.
If your equalizer can somehow convert speaker outputs from the head into line outputs, you can use splice connectors on those to the harness that runs to the amps in order to use the factory setup. I wouldn't recommend using factory amps with a modern head unit because you will eventually get distortion issues after a while, especially at louder volumes.
If going a DIY route I'd highly suggest getting wiring diagrams so you have at least an idea of where to start.