How can I make a Stencil from a color texture? At the moment I’m only able to make a Stencil from an alpha.
Convert your texture into an Alpha from the Texture Pallette, then use the resulting alpha to make your stencil.
But the resulting Stencil has no color information? I trid it and it was just an alpha.
That’s correct. There is no reason for a stencil to have color. The purpose of the stencil is that it either lets paint (or sculpting) through, or it doesn’t. As such, grayscale values are all that it needs.
Seems coherent. 
So is there a technique in ZBrush to mimic the Stencil workflow with a color map? I just wan to paint a color texture onto a map in projection mode but I don’t want to use the entire texture as a brush. I just want to be able to paint parts of the texture with an alpha brush onto the object.
One option would be to drop your model to the canvas and then to one side draw a plane with the texture on it. You then use the Cloner brush to copy part of the color from the plane to the model.