Using matcaps with texture maps
How do you get zbrush matcap materials to show through once you've applied a texture map to your sculpt?
The materials must be embedded into the texture map before they will display. If they aren't embedded then the map will only display the selected material, hiding the materials that you painted onto your model.
If you are creating a new texture map from polypaint then you can include the materials by making sure the Draw>Mrgb button is switched on before pressing Tool>Texture Map>New From Polypaint.
If you want to embed materials into an existing texture map then the simplest way is to install this little plugin:
Materials to Texture Map plugin
I hope this helps and let me know if you have any further questions.
Thank you so much for your help Marcus!