I've made them different ways, and you obviously have a choice of how to select your 9 squares:
Let's think of your choices as #1, #2, and #3 (which could be LIGHT, MEDIUM, and DARK, or the reverse).
With three fabrics you'll use #1 for the center square (which will turn out to be the small squares in the final quilt), #2 for the four corner squares (these will turn out to be the big squares), and #3 for the non-corner outside squares (these will turn into the rectangles).
You could actually use 9 different fabrics, but it will work better if you group them as one for #1 (light or dark), four for #2 (probably all medium), and four for #3 (dark or light, the opposite of what you've chosen for #1).
I used the same fabric for all my mediums (#2), and different fabrics (all dark) for #3...liked the effect.
But it's your choice -- no wrong choices here :-)