Hello Cathy! If you already have a specific room request in mind, I would suggest you go ahead and have your AAA agent add it to the reservation now. Requests are never guaranteed but you can be assured that cast members will do everything they can to grant your request(s).
As far as checking in online - yes, you should be able to do this. When booking through a travel agent or other 3rd party agency (i.e., Orbitz, Expedia, etc.) you'll need to access online check-in through mydisneyreservation.com. If you experience issues, please call your AAA agent for assistance. If he/she is not able to help, there is a phone number available for assistance - 407-828-7128.
(Side note for those who booked their vacations directly with Disney - please do not use the link above. Instead, please continue to use mydisneyvacation.com.)
Have a wonderful vacation! Diane :)