Set up your Model for Polypainting

Remember three points when using polypainting:

Polygon colorizing is enabled in ZBrush when the Tool:Texture:Colorize switch is on. It is off by default, so remember to turn it on before starting to paint.
Working without UVs will allow you to use more polygons and get more detail out of your model. Whenever possible, delete your UVs from your ZBrush model. You can always reimport them at the end of the process.
When rendering, ZBrush gives precedence to textures over polygon colors. This means that if a texture is active, then any polypainting you've done will not be visible. While painting, or to view your polypainting, ensure the selected texture is the Texture Off.

With this in mind, polypainting a model and producing a texture map is a simple process.

First, get a model. For this description, we'll assume that you don't need your UVs and can add them at the end of the process.
Set your subdivision level to 1.
Press Tool:Texture:Disable Uvs. This will delete your UVs. Make sure to have a back up OBJ file if you wish to use those UVs again.
Subdivide the mesh to get the number of polygons needed to match the map resolution you have in mind.
Paint the model, using alphas, masking, etc. Of course, you can sculpt at the same time you paint. Remember to turn on Tool:Texture:Colorize before starting to paint.

To Learn About Painting with Sculpting Brushes Click Here.

To Learn About Painting with a Texture Map Click Here.

To Learn how to Convert a Texture into PolyPainting Click Here.

To Learn About Baking PolyPainting into a Texture Map Click Here.