In short, you can use the app with bix files to do copy/paste between maps, resize maps, 'nudge' maps and so on. You need to reload a tweaked map with civ3XEdit to fix some tile-image and continent data issues... So it's a little rough round the edges but with a little care you should be able to get some very useful functionality out of it.
Apologies for making it in .NET and so requiring a chunky d/l from m$... but .NET rocks for developing, so err.. I'm not that sorry