There is no way to apply a colormap to a particular location only. In any one image, if you want two locations to have different colors, then the two locations must be given different values.
What you can do is create two images on top of each other, setting the AlphaData property of the top image to 0 in the place where you want the bottom image to show through.
In R2014a and earlier, colormaps are figure properties, so you would not simply be able to use different colormaps for the two images: you would need to convert one of the images to RGB, such as by using the File Exchange contribution freezeColors .
In R2014b and later, colormaps are axes properties, so you would not simply be able to use different colormaps for the two images in the same axes. However, you can use two different axes that are in the same Position to have them "stack up"
