Definitely check in upon arrival...we had 5 rooms booked and linked together for March. I did the online check in and my room reservation was separated. When we arrived, we were put in AB of POR and everyone else was in the Mansion section with their rooms all together. Of course, they had given us a complimentary upgrade to preferred and we had to tell them that we would rather stay with our party...Figures...lol!

They moved us as close as they could but they could not get us grouped next to everyone else.
The CM did say that if rooms need to be together not to check-in online. I think since I was the only one who used it that it somehow separated my reservation from the rest because she told me that my room was not linked to the other reservations. I know that they were originally because I booked all five rooms myself and confirmed that they were all linked.