I cant see my eyes,mouth, or put my clothing on! I have read the help section with no luck

I can see all of those things. Although why a naked ninja would wear the clothes part is ...odd. Isn't is part of the being sneaky? :)

The face parts need to be dragged above your base in your layers list on the left side of your screen. Your clothes may be subject to cache if you just now added them in. Waiting a bit usually solves this.