You need to get some short RCA cables that have MALE plugs on both ends. Use these cables to go between the harness and the amp. For the speaker wires it doesn't matter which wire you use for positive or negitive, you're just completing the circuit. You just need to be consistant. I used the stripe wire for negitive. The small brown box part of the x3 will not be pluged in. The x3 harness was made for mutiple uses and when installing the JL amp, it's not used.
Be sure to install a "line fuse" in the power line that you run to the amp from the battery. You can find these at any mobile auto store. I used a 40A fuse. This will protect your system.
If you need any more help feel free to ask. Good luck.