It's quite possible you can be near each other or far apart. Kidani Village is set up so that lock offs are next to dedicated villas. So it is possible. However, saying that it might not be that easy to do because prior guests may not check out and leave a dedicated 2BR and 1BR open next to each other for the days of your reservation. We had a family gathering in June and had two dedicated two bedrooms. We felt we were lucky that the two were just one floor down from each other. The kids often took the stairs to go visit the cousins on the other floor. But our five nieces and nephews were from ages 7 to 14 and we felt comfortable letting them make that trip.
Also if you requested a room near the lobby, a number of them are handicapped accessible rooms so that might keep your rooms further apart.
I'd say you can request they be together, but there's no guarantee.