I will take Equinox as my example.
In the index.php, you will observe<img src="<?php echo $mosConfig_live_site;?>/templates/<?php echo $mainframe->getTemplate(); ?>/images/blank.gif" style="border:0;" alt="" id="logo" />
You will notice it is loading blank.gif which is an image which is invisible.
The other reference to focus on is id="logo". This allows us to control it in the CSS#logo {
background: url(../images/style2/logo.png) no-repeat scroll 0pt;
}
Therefore, the logo.png will be loaded.