If my geometry isn't befuddled, I believe with a square or rectangular pond you have the ability to fold inwards or outwards to conform the liner to the walls. Are you taking the excess inwards (into the pond) or taking it outward so that all you have is the opening of the folded area at the corner with the excess tucked behind the water side of the liner? Try it with a piece of paper to see what works best. It is sort of hard to explain exactly, but if you pinch a corner of the paper from below so that it comes together on the top side, the outside edges come up and you wind up with a triangular shape on the outside. If you fold that against the outside edge all you'll have on the inside is the open seam of that.
I think most times people think of lowering the liner in and just making folds on the inside which is really the only sane way to do it with a round or odd shaped pond, but for a square and some patience and careful adjusting before you fill it with water, I think you really can make it so the liner folds almost go away. All you should have is a slight bulge for the excess liner behind the side of the pond liner you fold it behind since that side basically has a section that is 3 layers of liner when folded.
I'm not sure if I'm being clear, but hopefully this makes sense. Of course if you're already folding the excess to the outside, just ignore me.