when you UV map set up the floor part separate from the wall part. Here's a look at one I am currently working on:
the texture map thus far (done with photoshop):
the uv mapping process(done with cinema 4d/bodypaint 3d):
The rock and wood will be expanded to fill the texture space, once I get the building all layed out. This will give a better texture quality when the player gets close up. But, as you can see, there will be several different types of texture on the one .png image for the building. There will be 4: stone floor, stone wall, wood wall, and roof. I create these as large 512x512 and then scale and tweak to fit the uv map so it will look as best as I can get it.
Hopefully this makes sense.
Happy game making!!!