The DVDs, videos, and guides will almost always show the correct length to use (as well as whether you should use single or dual handle mode).
There are 3 lengths used. For suspended exercises, the system should be adjusted so the handles are 8-12 inches off the ground. Other than that, you will generally want the system either fully shortened or fully lengthened. Most exercises facing away from the anchor will be fully lengthened ones. Exercises facing the anchor will vary between short and long, but you can usually tell by the amount of movement that the exercise requires.
Still, as I said, the best references to use are the DVDs, videos, and guides.