It's probably easiest to separate the squares into dark, medium and light piles. I would pick just two of those to use -- darks and lights, or mediums and lights. Just makes it a little easier. Use the darks or mediums for the center and four corners; lights for the 4 other patches.
Are all of your squares different? If you have some that are alike, use 4 that are alike in the four corners. You can also add consistency by using the same fabric for each center, although that is not as helpful.