That sounds like a good plan.
do i need to include color in my array
It depends on what you want to do and how you have your two colour array wired up. Somewhere you will have the code that sends out your array to the chip, how do you feed that at the moment?
one color was just int pixels[8][8] but do i need to add a "layer" for two colors?
It depends on how you are going to use the array but one way is to use:-
char pixels[8][8]
If the pixel is off store 0, if it is red store 1, if green store 2 and if yellow store 3