Hi there, Carrie!
Online check-in for your Walt Disney World Resort hotel allows you to streamline the process at the check-in desk, and therefore save you some time standing in line. Additionally, there are Cast Members specially designated to handle those Guests who opted to use online check-in.
When you use this service, you are certainly welcome to make special requests. The online form does have a place to fill that information in.
Be advised, though, that online check-in does not mean that your room will be ready when you arrive. Standard check-in times do apply, even if you have gone through the online process. Additionally, if you need to modify your reservation in any way, you cannot do so through online check-in; you will need to contact the provider with whom you booked your Walt Disney World vacation.
Have a wonderful trip!
See you later, celebrator,
-Deborah B.