Paul,
I don't know how your template works, so I can't tell you where to put the code. However, I can tell you that once you find the location, all you need to do is add {JFBCLogin} into the proper file. If that text is being output to the user, JFBConnect will catch it and replace it with the appropriate login buttons instead.
I hope that helps explain, but if you need more information, just let me know.
Thanks,
Alex