Each module works on its own and can be disabled and enabled as you like. Later on theme support will be implemented, small addons that register a theme with mNameplates that can be applied on all modules at once.
Nameplates can be enabled and disabled for more in detail then just for friendly and hostile units. Some examples
Don't show nameplates for NPCs that are hostile and are of normal or elite type, but show for bosses.
Add names of NPCs (or players) that you do not want to see nameplates for.
Open configuration via LDB icon or /mn
http://www.wowace.com/addons/mnameplates/ for latest changes and news.