Overlay map usually is limited to lines and points, but you can experiment with areas too, you can for example define semi-transparent pattern for area.
There are many tools, free and commercial:
Creating and editing maps: GPSMapEdit, MapEdit++, Global Mapper.
Compiling maps: cgpsmapper, mkgmap, MapTk.
Editing TYP (skin): TYPViewer, MpaTK, ati.land.cz/gps/typdecomp/editor.cgi
Universal tool for all these tasks: Mapwel.