I would likely use modified truss head screws, or screws with washers and screw it just to one side of the plastic not all the way through both sides due to protrusion. If you’re concerned with that not being enough, maybe run a bead of silicone, e-6000, hot glue, etc in addition to anchor it.
If using the flashing I’d probably attach over the windows with a bead of sealant, then screws.
If using the flashing I’d probably attach over the windows with a bead of sealant, then screws.