The best option is to align the rooms while shooting. That way you can avoid the jumble of scans when you get home. This is accomplished while shooting by tapping on the move button with the target button set to room. The data associated with the panorama you just took will then be movable on-screen.
If you want to assemble room data at home the best way is to align them one-by-one in the order that they were shot. In Stitch, using the move and rotate room tool, select your first room from the top of the list and drag it off to the side. Then grab the second room and match them up so they overlap. Continue adding rooms together one by one until complete.
There is currently no way to move multiple rooms at once but I see what you mean.