So My figure has overlapping UV’s (body/head) but I can isolate those parts/materials so the map is not overlapping but…zbrush won’t let me create a ao or cavity map this way because it balks and says there are parts of the mesh is hidden!!
Is there a way around this??
If you split your model into two separate subtools (for the purpose of generating the maps only) then there shouldn’t be a problem. Alternatively you would need to alter the UVs so that the head and body UV shells occupy different UV tiles (such as 0,0 and 1,0). MME can then export the separate maps.
Different sub-tools I can do by Group Visible. 
The maps are separated by Materials, can you explain how I would put them on different UV shells??
You can’t define UV tiles in ZBrush, you’d have to use a different program such a Maya, or a dedicated UV mapping program.
If you are only dealing with one subtool that has overlapping UVs - i.e. the body and head of your model - then it would probably be simpler to create the maps yourself for that subtool and not use MME at all.
Okay, thought so…just double checking that ZB hasn’t formed a cool way to do that (yet!)