To confirm...
wannabeBelle, Carolyn1717, and AZDISNEYDVL are correct.
Officially,
For security reasons, only the Guest(s) listed in each room may check-in to their own room. A guest may not check-in to another guest's room even if the rooms are linked as a Magical Gathering (parties of 7 or less) or a Grand Gathering (parties of 8 or more.)
The only exception to this policy is if the party consist of 1 or 2 adults (age 18+) and any number of children (ages 0-17) from the same household who will not fit in one room or want separate rooms, i.e. a large single family.
Under no exceptions can a single Guest be listed in more then one room for the same travel dates. This may result in ONE or BOTH reservations being cancelled with or possibly without notice.
As long as the reservations have been properly linked at the time of booking, the rooms will merge when they download through the synch engine to the front desk from DRC. This will ensure the Resort will pre-assign the rooms as close together as possible, even if the Guests check-in at different times.
Note this will NOT ensure connecting (rooms side by side with a connecting door between them) or adjorning rooms (rooms side by side without a connecting door between them.) Connecting or adjorning rooms will normally not be proactively offered or assumed, the Guest must ask for them. Also, remember not all rooms types can connect or adjoin.
Connecting Rooms may be guaranteed only when there are 1 or 2 adults and any number of children ages 3-17 from the same household who will not fit in one room, or want separate rooms. In all other cases, it is only a request and will be treated as such.
Also please note, one does not need to request a late arrival note with the Disney Reservation Center unless the Guest is expected to arrive after 11:00 am on the day following the scheduled date of check-in. If a Guest has a deposit on the reservation, the Resort will hold the room until check-out the following day.