You will need an amp wiring kit, you can pick one up at WalMart, Best Buy, etc. They usually run around $30-60 depending on the gauge of the wire. You'll probably want one rated for around 700-750 watts.
There are three power wires:
1: Main Power Wire - which attaches directly to your battery.
2: Ground Wire - which you'll need to find a suitable ground in your car (you can just find a small hole into which you can use a small screw, but you need to sand off the paint first so it will attach directly to the metal).
3: Remote Turn On Wire - This wire goes directly from your headunit to the amp. It turns the amp on when your radio is on and off when your radio is off.
Then there are the RCA cables: They just plug into the back of the headunit and the amps, in the red/white ports. In your case, the wires will plug from the headunit to the Pioneer amp in the input ports, then a second set of wires from the output ports on the Pioneer amp into the ports on the AudioPipe amp. (ie: [headunit]==[Pioneer]==[AudioPipe])
Finally, there are the speaker wires: If you have hooked up any set of speakers before, you've basically done this. Just take the speaker wire and go from the channel output terminals to the terminals in the back of the speakerbox.
The speaker wires and power wires are attached by loosening the screws on the side of the amps (left for Pioneer, right for AudioPipe), wrapping the bare wire around the screw a bit and screwing it back into the terminal (make sure the wire is UNDER the small plate though).
Personally, I've never used a cap. I believe it is attached on the Main Power Wire, before the amp. Just snip the power wire and attach the cap in-line. (ie: [battery]---[cap]---[amp]) If someone could confirm or deny this, please do so.
It is fairly a straight forward install. I've done my fair share of simple installs while I was younger. The whole process should take no more than an hour. Honestly though, I don't know why you have two amps. For your situation, I'd use only the Pioneer amp, unless you're planning to add full range (door) speakers to your setup. Any more questions, feel free to PM me (or look out for SquillyB, haven't seen him on in a while though).