Jack, I wouldn't bother covering it while towing. I've seen too many "Parachutes" out of covers and/or awnings. Just roll up the passenger window, and if you haven't taken out the glass on the drivers side, roll that up to.
Otherwise, treat it like you would if you were going to drive it. Attach the window net, belts, and if your going to use the inside of the car storage, just make sure everything is tied down and secure.
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Tim Linerud
San Francisco Region SCCA
#95 ITB GTI, GP for 2002