Ted,
You're right! If you're using the JFBCLogin module, we don't mention how to get rid of the existing button. I just updated the guide with the text below. Hope this is what you're looking for, but if not, just let us know:
If you're using the JFBCLogin module, you should also remove the inclusion of the normal blue Login With Facebook button by search for the following code and commenting it out (put two slashes in front of it - "//"):
echo $fbClient->getLoginButton($buttonSize); ?>
Good luck,
Alex