Well, I still need the answers to the above questions, but here's a general overview, assuming no fish are in the pond.
1st, drain it. without knowing what kind of pump you have, cant say much more, maybe use the pump, maybe a syphon, maybe buckets, uggh.
Then get in there and remove all the waste and gunk from the bottom. ( this stuff is pretty yucky and smelly, but it makes great natural fertilizer for flower or veggie gardens). don't use anything sharp to get the crud up, you dont want to damage the liner or plastic. no metal tools at all. kid size plastic shovels work pretty well, just be careful.
Actually, without answers to the previous questions, I pretty much have to stop there. Get back to me on size, liner, pump, filter specs, and I can go much further.