the best way or the method i use is actually the two already mentioned, when erasing parts of the c4d you erase the parts that may clutter the focal or detract from the flow in the sig or piece of work, sometime the colours might not match or the part of the c4d is too light or dark, so again erase.
When using clipping masks they can look cheap because sometimes it doesnt add anything and just looked like something add to the art, so when you apply the new image try to transform is upside down or back to front so the person can tell that its from the same piece of art but they cant match it up. This make your sig look more complex