Decided to look on how to link the two programs since I'm lazy (I can say better I find useless to write more time the same data when using digital information we should be able to transform it).
There is the possibility to create a character sheet export xml that can be used to create a new tocken based on the information from PCgen so you can keep info from your PC in pcgen that is surely the best of the two, but can use MapTool for mapping during the session.
Creating the xml in PCGen is quite easy and there is lots of usefull data there.
All you have to do is than placing the saved file inside a previously saved rptok file.
To satisfy my laziness I'll try to automate the import in MapTool.