Joe,
There are a bunch of threads and posts relating to main drain issues. Just a couple very recent ones:
http://www.poolforum.com/pf2/showthread.php?t=5912
http://www.poolforum.com/pf2/showthread.php?t=6038
and if you keep digging in this forum you'll find a lot more. I don't have a MD so I'm speaking from what I've read and some knowledge of freezing. The skimmer is the critical thing so that line has to either be dry or filled with RV antifreeze. The water in the MD line certainly has to be removed above ground and below you should lower it as much as possible and then seal the line with the valve. You'll find more details about how you do this in recent past threads.
Al
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