We usually mound the edge a bit when finishing the liner on a pond. If the liner is an inch or two higher than the soil level at some point between the pond and the outside edge where it's cut, then rain water will wash away from the pond from that point, and outside material is less likely to sift through the rocks into the pond. I also tend to leave a fair bit of margin on my liner for future adjustment, under the rocks and boundary material.
I have seen people mortar in their edging rock as well, placing a layer of mortar directly onto the liner and pushing the rocks into it, which seals the edge and pushes the overflow boundary up above the where the liner is visible. I don't know how well that works over time, though, on the flexible liner surface, as I haven't done it myself.
For cleaning up muck on the bottom, I lower the level of the pond in the early spring and mechanically remove, but I tend to prefer a little muck down there for buffering and fish health, unless I have a bottom drain installed.
I've seen others use pool bottom vacuums and hoses with a good siphon going to clean out debris on the bottom as well.
