I always cut off the excess film at the edges with a hot knife and then fold the new edges over and bond them down. Most of the load on a cuben panel is borne by the whitish dyneema fibers inside the laminate, but the integrity of the outer layers of film is important, too. I soaked a bit of cuben in a methanol/NaOH solution once, to create some microscopic pitting and fissures in the film, and it was much weaker. Mylar film has a property that is familiar to anyone who has torn a space blanket: a tiny nick can initiate a tear that can zip through the material under almost no load. Along the edge of the film on a cuben panel are millions of microtears that can propagate under load. A BPL poster with access to an Instron tensometer confirmed that you can dramatically increase the tensile strength of a strip of cuben by folding the edges over, to reduce the load at the microtear-riddled edges. This evidence also supports bonding or taping as opposed to sewing cuben, because sewing creates a line of jagged punctures (edges) which weaken the film.
So, I'd recommend cutting off the excess film, folding the edge over, and taping or bonding it down.