Hmm, I guess that message does imply that multiple map scenario files would be supported.
I did intend to do that if I could figure out the file format for multimap scenarios but I never did. It took me over a year to figure out a formula for locating the city block.
At this point with CIV III on the horizon I don't plan to support multi map scenarios.
In case you were wondering why, Civtweak never gets near the city data, so that's not a problem there.