They make shrinkwrap doors for that purpose.
http://dr-shrink.com/products-page/zipper-access-doors/
1) Tape the door where you want it located using shrinkwrap tape. (Basically just tape around all four sides)
NOTE: There is an Inside and Outside to the door. The Outside is the side that has the covering over the zipper to kep water out.
2) Unzip the door.
3) Cut the shrink wrap inside of the zipper.
You're done. This is a great way to get work done in incliment weather. The shrink holds in heat nicely. I do all my work short of the spring wash and wax with the cover on. I take it off just about the same weekend I'm ready to launch, or when it gets too hot in there (whichever comes first).
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