What you COULD do, is try copyrecting the footprint texture. You could have a texture overlaid on top, have it painted white, and set to add mode. Now, simple copy black footprints to the texture. They should show the texture below. If that's no good what about....
Have the white texture at the bottom and a blank texture on top. Everytime you want a footprint texture, draw the rocky ground texture to the blank texture, in the shape of a footprint.
Have the white texture at the bottom and a blank texture on top. Everytime you want a footprint texture, draw the rocky ground texture to the blank texture, in the shape of a footprint.