Hey guys, Trevor from RPTools here! I'm the primary developer of MapTool, thanks for the interest :)
Some context, MapTool started out as simply a battlemat replacement, which is why it is more map centric than character centric.
The past year or so of development has changed the direction to adding more character centric features. Unfortunately, as Azhrei mentioned, the documentation isn't keeping up, and there is a great need for polish. Fortunately as we near 1.3 completion we're working on both of those elements.
I'd be happy to field any questions here or offline that anyone has about specific features, clarifications, or issues. We also have a very, very (somewhat rabidly) active and friendly forum, feel free to drop by and ask questions there too.
To answer the question about the CharacterTool and Maptool, currently the various tools do not interact with each other, unfortunately.
We're finishing out the 1.3 build and will begin 1.4 shortly which will focus heavily on fleshing out the non-map related features and simplifying the interface. We welcome any and all feedback, in fact most of the development is community driven.