The ModPath is the path to the folder containing your modified files. Only set this if you have also modified XML or python files. Otherwise, save your WBS file to PublicMaps (found in your Civilization 4 directory\PublicMaps) and leave this line blank. If set, it will force the scenario to use the settings in the mod folder defined rather than the default settings of Civilization 4.
EG: ModPath=Your Civilization 4 directory\Mods\MyMod\ (replace "MyMod" with the name of your mod)