If you go over your target, the points are first taken from any activity points earned (if any) since they are only good for that 1 day and then from your flex points.
Also, I would encourage everyone to at least think about eating some of their activity points. Your body needs fuel to recover from the exercise you just did. The statement "If you don't use them, you should see quicker weight loss" is not true for everyone for this reason. Besides, if you can eat a little more and still lose the weight why not?