The window "Mapset installed" of MapsetToolkit operates on Windows registry only - the part of registry that is read by BaseCamp and Mapsource to find an installed map. Here you can install a map, remove a map or edit paths to parts of a mapset, like for example TYP file.
The rest of MapsetToolkit is a helper to create mapset - compile preview, create TDB and index. It is a GUI overlay for program cpreview.exe, which is a part of cGPSmapper. There is option "Install in Mapsource", which adds registry keys after compilation, but if you recompile your map, then most probably registry doesn't have to be changed.
I don't use MapsetToolkit for compilation, I prefer to run cpreview.exe from my scripts. For me the "Mapset installed" part of MapsetToolkit is most usable.