You should not have any problem with a 6pm check-in. You may just want to let CRO note this in their computer system. We arrived once around midnight (flight was delayed a couple of hours) and had no problems.
You can ask for a late check-out - I think the day before you leave. I understand they will only give you until 1pm or so if they do not need your room. If you want longer than that I believe it is a 1/2 day charge.
What you can do is have your luggage picked up and the resort will store it for you until you are ready for your trip back to the airport. All Disney resorts do this for their guests.
