The best piece of advice I can give you regarding online check in is this -
If you have a room request that will make or break your vacation, do NOT do online check in. Check in at the front desk so you and the CM can go over the available inventory and select a room that best meets your needs.
If you don't have any particular room requests then doing online check in is fine. I've done it for every stay but one since they offered it (they wouldn't let us do it for opening day at BLT) and I have always had a room ready when I arrived and the rooms were in very convenient locations. I never felt I was getting the bottom of the barrel when it came to room assignments.
While you can change your room assignment after you've done online check in, it does take time. In fact, it takes as long or longer than if you'd waited and done regular check in in the first place. So far, I haven't had a reason to make a switch, but I've been in line behind people who have - not fun.