Joel, do you have an overflow? If so, no need to drain any water. And, if you don't have an overflow, that would be a priority now, before Sandy hits, if at all possible. It's as easy as making an inverted tent in your liner on the edge somewhere, or that's how I did it. If the water gets to that level, before it goes over the edge, it seeps out between the rocks at the place that is the lowest on my pond. Of course, my pond top edge was not exactly level with the water, so finding the lowest edge was easy. LOL Before I had the stream and goldfish pond added this summer, I put a small "slide" below where the water would drain, and then a short piece of pipe to direct the water. I weighted the pipe down. I only did this when heavy rain was predicted, to make sure the pipe stayed in place and the water drained out and away from the pond.
Murphy's Law says if you drain your pond down, you won't get any rain. If you don't drain it, you will get a boatload! Your choice, but easiest is to have a place for the water to naturally overflow if possible. Good luck!