One of FT's strengths is that it keeps its world data on a globe. That globe can then be reprojected as desired and output to CC3 for more detailing. Individual map segments will be based on the same information as the original whole-world map and so will be consistent across zoom levels (allowing for distortions produced by the map projection, of course). FT offers a view management system that allows you to zoom to a particular view on the globe and save that view in the FT file for later use. This technique allows you to set exact projections and scales for a whole set of output files.

FT also offers an "Export Multiple Files" feature, but I strongly caution against its use. Aside from a few bugs with the output, that particular feature doesn't offer any control over where the individual files get split. It's easy to generate thousands of useless maps in just an hour or two. It does offer some nice things like automatic linking of the output files, but the other problems far outweigh the benefits. I'm not sure what the guy who wrote that bit of code was smoking, but I sure don't want to smoke any of that every again.

Some of FT's fractal facilities start to look ugly as you zoom in close, but there are a couple (RMF with Perlin's Improved Noise, for example) that can be rigged to zoom in to generate a map that's a mile or so across. Most of the others start to show serious artifacts as the map gets smaller than a couple hundred miles across. What you're going to do with the map will dictate how badly the limitations affect you.