Yes, you will still be waitlisted after you check in. Check in as early as you can, use on-line checkin. The checkin order will determine where you stand on the waitlist if you are going to clear at the airport. If you check in early, keep an eye on your reservation - there is a well known problem where your upgrade clears (you get an EasyUpdate) but is not seen by the gate agents. Ask them to check for it in the reservation system or have them to unload you and check you in again for the upgrade to show up.