Whenever I've used vac canopies, I've usually put some blue-tak up inside them when cutting and trimming. This helps to stabilize the canopy and keep the whole thing from flexing while you handle and cut it. I've also read that some folks use modeling clay.
You may also wish to use some sort of tape as a cutting guide to help prevent the blade from slipping off track while cutting. I use 3m green masking tape which is plastic and a bit tougher than regular masking tape.
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