FT Pro (version 2.x) is much, much better in the richness of its editing tools than the original version 1.x. I would recommend upgrading if you can because many of the tools in FT Pro have no equivalent in FT1 (rivers, basin fills, incise flow, pre-scale offset editing, remap altitudes, and so on).
As far as starting a world, it is much easier to start with a world that's not flat than it is to start with a flat world and go from there. Pre-scale offset editing in FT Pro makes life much simpler when painting because it works with the continental shelf and scaling rather than fighting them. It wasn't a clean implementation and the number are a little fiddly, but it's not too awful once you get used to it.
This is the old prototype GIF example of the concepts involved:
http://www.ridgenet.net/~jslayton/Tutorial1.gif
The actual steps I used in the example for this thread were somewhat different than shown in the GIF and I'll see about getting them written up.