I wouldn't do online check-in (personally). It makes it tougher for the CM to switch rooms to meet your requests if you are not placed somewhere you want to be. It is not advised for those who care more about getting their "ideal" room than speeding through check-in to do it online.
As for low vs higher floors, that comes down to preference. Personally, I like being elevated and having a balcony as opposed to a patio. I would be wary of the top floor rooms (can't remember if there are 4 or 5 floors) since those dormer rooms have smaller, enclosed balconies. Some people do love dormer rooms, though, due to their elevated ceilings. Here again, it comes down to personal preference.
I already suggested this to you in the GF FAQ, but I would request Conch Key due to its convenient location and lack of construction views.