/includes/templates/your_template/common/tpl_header.php handles the output of the logo which is defined in header.php. It is a foreground image. Adding a background image will give you two logos.
The default stylesheet has references to #logo, but mostly grouped with other items. You can specify position, margins, padding etc. for #logo and #logoWrapper; just don't try to use bg and fg images at the same time.
The definitions in header.php specify the filename and area reserved for the logo. You should set them to the actual dimensions of the logo image you are using. A discrepancy can sometimes cause errors in the display.



