The ISO harness carries the wires for
constant +12V (input)
switched +12V (aka as accessory) (input)
ground (input)
amp remote turn on (output)
phone mute (input)
dimmer (input)

Since you want to keep your stock HU, you need to identify the wires in your cars harness (likely not to have amp remote and phone mute, as they normally go to aftermarket accessories [amp and handsfree phone kit] not normally present) and splice the ISO connector into those wires. I'd recommend soldering and shrink tubing.
You'll need to run a new wire from the amp remote turn on on the ISO harness to where your amp will be located - can be routed along with the RCAs. Even if you don't have a handsfree kit or mobile phone it might be a good idea to extend the phone mute wire to someplace easily accessible if you ever would install a kit (or use the phone mute for something else, like making a radar detector hush the empeg...)

Then there's the question of if the power and ground wires are good enough to handle both HUs at once - I'd try it out before running new wires though, but if you get problems with ground loops/alternator whine, consider upgrading those wires.

You'll also need to run power to your amp - that'll require much thicker wires than the ones that go to your HU. Exact requirements depends on what wattage your amp is, but I wouldn't go with less than 8 awg. You'll need a fuse holder close to the battery for this wire. Ground the amp to a good ground and make sure there's no paint between the ring connector and the metal of the car.

This site has a wealth of basic information regarding car audio and car electrics.

/Michael