Wrestling with the underlay

Use underlay designed for ponds, because it doesn't rot and its close weave resists root damage, unlike turves newspaper or old carpet. If you have to replace the liner later for some reason, the underlay will still be serviceable.

If the hole has water in it then it's no problem, just push the underlay down into it. Cut off some of the excess at the edges, but leave the final trimming for much later, once the liner is on top and the pond filled with water.