Maybe I am mistaken, but the only way to export an object with multiple faces is to have a single color?  
What are t he ways around this?  ???

Shockwave3D does not support multiple colors, but you can use a texture that contains a color palette and apply a "cropped" version of the texture that contains only that color. Have a look at the end of this tutorial for more information: http://www.amabilisplus.com/3DCanvasDocumentation/tutorialmstsmaterials.htm

Richard