Depending on your plumbing, there are a few things you can do. A lot of people, from what I have read, place foam down the piping for the main drain. This usually, only works when connected with the skimmer.
Below, please find a thread (Post # 10) which describes the experience a member has had with a pancake compressor and how to work more efficiently!
Closing: blosing out lines, water level and then some
Please note that it takes an extended amount of time before any damage can be done. Therefore, you are safe for a while. Try using the compressor and allowing it to run, not shutting off and building pressure. If you start seeing little tiny bubbles near the main drain, allow it to run for a few more minutes and then close the valve, shut off the compressor, creating an "air lock". You may need some goggles to see clearly towards the bottom.
If you do not mind spending around $350, you could purchase the Cyclone + accessories, which IMO is worth the $$ not to have any aggravation during the closing time. Please keep us posted!