The way in which your SAT score is calculated depends upon the college you're applying to; however, averaging scores is not a common practice for undergraduate admission exams.
The fact that you're thinking about this most likely means that you're the type of person who likes to be prepared. And that's great, because preparation is the key to doing well on either the ACT or the SAT.
First things first: the GPA is more important than standardized test scores. Colleges recognize what you do every day for four years is a more accurate measure of your intellectual curiosity and your academic focus than is a test that you take on one Saturday morning.
Talk to an admission representative at the school and ask that question. If you have extenuating circumstances, such as a learning disability or illness that contributes to your low test scores, the colleges might take that into consideration.
A student should take the most rigorous course load available in which he or she will be successful. A question that is often asked is, "What if I get a B in an AP course when I could have gotten an A in an honors course?"
In some cases you'll be required by a college's admission process to take specific SAT Subject Tests. Here are other reasons to take the Subject Tests.