Okay, this is from my own personal experience and I can guarantee it works, and works well. You're gonna need some things:
1. Amp Kit
2. After Market Amp
3. After Market Subs
4. Speaker Wire RCA Plugs (You can get them at radio shack)
5. A Drill (Not required but makes it easier on you)
First things first, disconnect the negative terminal on your car battery, then unbolt the old RF sub from your trunk. It uses a size 10mm socket and I believe there are 3 bolts (maybe 4). Then disconnect the wire harness connecting the RF sub to the wires (its on the back of the sub near the top). Dispose of your old RF sub in any fashion you'd like. Next cut the wire harness off of the 4 wires. Okay the wires are as follows: Green is L+,Yellow is L-, Blue is R+, and Red (or in some cases White) is R-. This is where the RCA plugs come in. Take some of the speaker wire included in your amp kit and use it to lengthen the 4 wires. How RCA plugs work are that the middle prong is your positive, and the outer shield is your negative. I got the solderless RCA plugs that allow you to screw the wires on. Basically all you had to do is remove the RCA plug's cover and screw the positive cord to the middle screw and the negative screw on the outer one, then pop the cover back on. Do this for your Green and Yellow, then your Blue and Red(White). Your RCA inputs to your amp are now complete.
Next is running your power wire. This can be easy or difficult depending on how you do it. I'd start at the engine and work towards the trunk. Facing the car to your left in the very back of the engine bay against the firewall there is a little black rubber circle or grommet. It is VERY hard to get to without removing parts but it can be done (because I did it). The easiest way to remove it is to simple drill through it (and through the fabric behind it) then pop it out (or leave it if you don't have a replacement to put there that would be included in your amp kit). You can use a knife and pliers to eventually get it off (which is what I did) but it was a MAJOR pain in the ass. Next put your cord through the hole and walk around to your passenger side.
Now you need to run the power cord through your cabin. Doing this is very simple. First remove the bottom of the glove box. There are some pop out screws that come off very easily. Look far up in there and you should see your power cord, grab it and bring it down. Next pop the trim off along the passenger front and side doors. You should see a bundle of wires already there wrapped in black electrical tape. Simply run your power cord beside these. When you get to the back seats put them down and you should be able to funnel it up the side (inside the trim) to the trunk. After this is all done put your trim back on.
Basically you're all set now, you have your power wire and RCA inputs ready to go. Just follow a simple amp install guide for the rest of the info on how to hook up the amp to the subs.
One thing remains, the remote amp power on wire. This posed a problem for me as I had no idea how to attach this to the RF MMCS headunit, so I didn't. Instead I connected it to the 12V Power wire used to power the amp and wired a toggle switch to it which I ran through the driver's side trim. Works like a charm.
How to: Installing a 2nd Amp w/ RF System
