I would have to say that cardboard is a good bet. Lay it under the panels, and trace it. If you are doing it higher up, start with a surface at the height you need it at. From there, take little pieces of cardboard to get the outline. Basically, use long strips. Run the strips the width of the car. Push them all the way into the panels, and tape it. Continue doing this all around the panel. This should give you a template.
Unfortunately there isn't a super easy way to make it fit. Just take some time, and trace/scribe it out. Find some scrap wood or something to make a test piece. Once that's set, make your final product.
I am doing all fiberglass in my trunk, so I didn't have to trace anything. Hopefully somone that has done this can give you a better idea on how to go about this.
Curt