You have to link the reservation to your account. The hotels.com reservation number is not (unless they have changed things very recently) a number that the disney accounts recognize. So you have to contact hotels.com (call or email) to get the 12-number Disney reservation number. It might take them a couple hours to get it (DH has status with their 5star program and they do a lot for him, but it still took them a couple hours to get it) but they can get it and can get it to you.
Then you enter that in to associate the reservation with your account.
Our trip was in Feb, and we had a 2 night reservation on "free" nights through hotels.com there. During that time Disney's systems and site were in even more flux than currently, and even though I did online checkin, they were missing DH's name and DS's names. They were listed as Guest MyLastName, LOL. They were also missing the CC info I had input during the online checkin process. BUT the important stuff, that being when we were arriving and whatever I had checked off while checking in, did get through. And having the CC info missing wasn't unique to the reservation made through hotels.com; it happened more than that during our long stay with 3 other hotel checkins, even though I had booked directly through disney (well, DVC) for them.
So get that number, associate it with your account, try to fix things if there's anything odd (hotels.com only has space for ONE name...just in case you can't get that fixed, put the name of the adult guest that you KNOW will be there to check in at the hotel, just in case someone is delayed by work or whatever), and go about your checkin!