I believe you can do it both ways. We had 2 rooms at Pop as one reservation and a request that they were connecting. The CM did it as 1 to ensure we'd be connected. We could have done 2 separate ressies if we wanted to do different packages on the rooms (for instance AP rate on 1 room and FD on another) and they would try to do them connecting but as the sep ressies they couldn't guarantee that.
Anywho, in the end we switched to ASM FS because for what it would have cost us to get a cot and fridge added to the Pop room so my 3 wouldn't share a bed (and we wanted a queen bed for us) the price ended up the same.