Using Masks:
Start with a photo selected
* Change to Region Painter tool
* Paint regions you want to change
* Change to Selector tool
* Clone (this clones only the areas of the photo covered by the mask regions)
* Apply contone colours

(The general model is that when you're in one of the mask or region tools commands like Clone will _affect_ the mask or region that you're drawing and when you're not in one of the mask or region tools commands _use_ the mask or region that is present. Unfortunately the UI doesn't make this very clear.)

Phil