Sometimes you ask: In the e-mail body, how will I know or the system knows what is the right place to put the member name or the site when using the %s for all them (username, site, and link) if all them use the same symbol %S? How does the system know each one? Does it have some order? How does it work?

Here is the Answer:
It is defined in the controler.php file at yoursite/components/com_alphauserpoints. If you check the line 511 (version 1.4.0) you will find the order it is defined at: $body = sprintf( $msg, $SiteName, $sender, $link) . " \n" . $custommessage;