You should never drain a liner pool. Draining it can cause it to become brittle. You may have already ruined your liner if you have drained it. Should you go ahead and refill it now? I don't know if it will matter at this point. My guess is that your liner is probably shot, but somebody else may have a different opinion.

As far as how to keep it from getting nasty over the winter -- if you close it properly and adjust your chemicals before you close it, the water will stay clear over the winter. You may get some debris in it, but that is easily cleaned up in the spring.