Depends a lot on the size of the holes. If it's just a few (or a bunch) of small ones you haven't hurt the integrity of the polyspan enough to worry about so you can simply dope and overlay some light or medium silkspan. It's much easier to cover/sand/feather in and "hide" the silkspan than another layer of polyspan. If it's a large area, just cut out the entire bay and redo that section with the Polyspan, overlapping the perimeter by a comfortable margin.