Yeah you can mix and match anyway you want you could get real creative with this as I mentioned earlier I've seen ways for the Falcons to get new uniforms with their color rush.
The only thing that needs to get patched right now are the shoe colors with the color rush tops. When you choose the color rush top you can only use black and white shoes instead of team colored shoes. If you choose the color rush pants without the color rush top they will change. So this needs to get patched by EA at some point.