This is probably a stupid question but can you bake and export multiple materials on the one object.
i did have a look at the baking matcaps into textures and thought this might be the way but that method needs the image plane plugin to work and i cant get it to load on zb4. So i presume there is another way of doing under another name or some such as i cant find it in the documentation at all.
what i am trying to do is have a guard on the arm of a character that has a layer of banged up paint with an under layer and then a shiny/ rusty base metal underneath and i am a little stumped on how to get it into maya from zb.
Any chance someone could point me in the right direction? 
A shiny/rusty effect is something you need to create with a Maya shader. Those sorts of effects cannot be conveyed through a texture. A texture can only contain color information, that then works together with the material to create what you actually see.
Even if you were to bake the materials in ZBrush, all you’re going to get in Maya is basic, flat color. You’ll still have to set up your shader in Maya to create the specular and anisotropic effects necessary to make that color look like metal.