How do I change the order of the rooms?

Drag the rooms into the order you want in the tour's scene list. On the Tour tab, each row of the list has a handle to drag and move buttons; dropping a row, or pressing a move button, saves the new order at once. The scene list on the Panoramas tab works the same way.

That order is the order of the rooms in the tour's menus and in its next and previous buttons. To sort rooms into floors or areas as well, put them in panorama groups: see Organize scenes into panorama groups.