Since tons of you have helped me with my idiot questions I thought I'd post this image which explains how to load a program into a Colorduino using an Arduino.
First take the main CPU chip out. Then use jumpers to connect:
You can see these in the attached image, even though some wires go out of the frame, just follow the colors.
I used an external 6V supply for the colorduino (slider set to "terminal") so that I did not have to pull to much power from the USB of my portable. Hence the brackets in the 4th connection listed above.
Anyway, I hope this makes it clear to others following the same path.
Ah, one other thing you might need to know. When you plug in the 8x8 matrix on top of the colorduino the "1" on the matrix should correspond to the "1" of the blue section on the colorduino.