So much data, thanks so much for the feed back and testing the case senerio for me. I was about to try that next weekend. I think i'll have a good chance at my workflow now. I love this product so much right now. 

I got home a little earlier :) And it is working!!




BTW Renaming materials and creating new is also possible. CC pops a warning, but lets it slide. So actually I made 2 materials for each eye.

Sweet!

Here is mine, and also some custom CC eyes for anyone who wants to download them. Just load your Substances from Substanceshare.com. There are a few different eye makers there. You can use the same Substance for each eye, but I did have to load a different one to get it working. Not sure if I just made a mistake or not, but it works well.

One eye is "Eye", and the other is "Cornea". You really don't need both materials on one eye.
https://share.allegorithmic.com

That's cool! I just looked and actually have 4 of them substance ready now (originally I changed materials in iClone).
Meaning we can do whole lot more. Splitting body mesh into different materials if necessary - accenting on specific parts (oh boy there we go again :)) 
So what's next? A different nail polish style for each nail? :P

Is there a way to get proper Seperated UV's on the Obj export? I'm trying to bake the texture paint from ZBrush to the OBJ but the mesh has all the UVs overlapping and Importing the FBX in ZBrush is unusable for sculpting on. Maybe I have to do some kind of baking in substance or something? 

Never mind: https://blog.reallusion.com/2016/07/25/speed-sculpting-a-character-with-zbrush-character-creator/