ok, first, I would worry about getting the entire city from one map to the other. (the square map thing isn't a big deal, just make the terrain round or what ever shape you want and ignore the other space by using the boundary tile in the terrain Palette)
#2: First go to the Terrain palette and drag your mouse over ALL your city. Then do Ctrl C
After you've done that go create a new map with the size and tiles you want. Then do Ctrl V and place the terrain where ever you want your city to be.
#3 Now go back to your original map with your city and go to the Doodads Palette.
Then, Select ALL the doodads that make up your city and Ctrl C. Go to your new map and do Ctrl V. Place the Doodads directly over the terrain. (it may take a few times to get it right and you can always select all the doodads and delete, then do Ctrl V and try it again.)