I was hesitant to do online check-in as well, but ended up doing it. We arrived on a Thursday at 5PM. Before checking in online, I called a final time and asked the phone rep to add my requests to the reservation. About 3 days before our trip, I sent a fax to the resort with my requests/preferences, arrival date, and confirmation number. In it, I wrote that I understand it is just a request and there are no guarantees. I then resent the fax a second time the following day.
There was no line for online check-in or regular check-in when I arrived. Honestly, I never saw much of a line during our stay. My check-in only took 2-3 minutes since I didn't have many questions. When I checked out, I had to wait for another couple to check-in and the process definitely takes longer if you don't do online check-in.
My recommendation would be to check-in online to save time, call again with your request today, and fax your request to the resort tomorrow (fax number is on the 1st post here). Then, have a resort map ready when you arrive and if you don't like your location, you can always ask if another location is available. You are not locked into a room by checking in online. One thing I learned on our trip is that Disney has excellent customer service and will strive to satisfy every customer.
Have a great trip!