We are checking in to our WDW resort the same day as relatives. I called Disney to have both room reservations linked as the same traveling party and also requested connecting rooms (which I know is not guaranteed).
We will not be arriving at our resort until late afternoon. Is it better, worse or “makes no difference” to check-in online in the morning in terms of our chance of getting connecting rooms?
Shouldn’t matter
Your travel-with number is the more important thing and they will put you near to one another if that’s at all possible
But don’t select anything for the room request when you do online check-in.
I’ve heard from those that have worked front desk, that when you do online check in, it negates everything that has been requested over the phone or via fax. The reason ostensibly being that room assignments is a totally separate department and has no connection to the resorts or the reservations line. Either way, I always advise my clients to check in at the front desk (even if they have done online check in) to make sure they get what they have requested.
This is pretty ridicilous if true, but my experience actually supports this theory… Last time I requested a connecting room well in advance, I didn’t get one despite them being available. When I asked the front desk, they moved us one floor up to connecting ones, so it seems like my request was never acknowledged, and I checked in online… 
We know the room assignments are done centrally now. That in itself doesn’t “explain” anything. So the realistic explanation is the one we’ve suspected for a while.
There’s only one data field for room requests.
The on-line check-in selection will fill that field automatically. If anything is there already it will simply over-write the existing request. That’s standard data entry coding. So not really ridiculous at all.
If you call in, or contact Member Services (for DVC members) the CM will type into that field. If you’ve already done the on-line check-in you they might add to what’s there or over-write it.
If you use TP and get an email sent in then that depends on whether it is picked up and recorded. And if it is, again they might add to or over-write whatever is there already.
I assume most people do on-line check-in later than making any room requests another way. So if they do and they select something from the drop-down menu then that will over-write the previous request.
We also know some resorts used to be better than others at fulfilling room requests. Some were well known for binning anything that came in by fax / email. Now that room assignment is done centrally it’s likely that some CMs working there do record room requests, and others won’t. New CMs will follow whoever trains them.
So for actual recording room requests the likelihood of them being done is
on-line check-in >. call in / chat. > TP requests
But of course the on-line options are much less specific and in some cases total nonsense.
So the advice to never choose from the on-line options still stands if you’ve done any other type of room request. Even though it’s the only method that guarantees your request will be recorded.
Whether you get your room request comes down to luck.
We arrived back home today after 5 nights at WDW.
As another data point:
(1) I called WDW in 10 days in advance to request connecting rooms. I did not make any other room requests.
(2) I did not do on-line check-in.
(3) I checked in at the front desk late afternoon.
And … we got connecting rooms.