Looking at your site briefly, you have a number of HTML and other issues you will probably want to address prior to the Comodo logo.
Your website specifies XHTML 1.0 Transitional
In XHTML all of your "tags" must be balanced. This means you need a matching end tag for every element. This includes tags like "<br>" and "<img>" which typically are written as "<br />" and "<img />" in XHTML. There are also some unbalanced "<div>" and other tags.
When you use an attribute (href, src, rel, etc) these need to be in the format src="https://www.worldpay.com/images/cardlogos/mastercard.gif". Note the double quotes. No no spaces inside the quotes. You are not allowed to have more than one "id" attribute (you have two id="comodoTL").
Inline javascript should be inside a CDATA block to tell the browser to not parse the script using an XML parser. Most modern browsers will strip the javascript before parseing, but never hurts to cover your bases.
<a href="http://www.instantssl.com" id="comodoTL">SSL</a>
<script type="text/javascript">
//<![CDATA[
TrustLogo("/images/tl_transp.gif", "SC5", "none");
//]]>
</script>
These issues need to be addressed to ensure the web browser knows how the site should be rendered.
A couple of times I also saw problems with your footer not being generated. Not sure what the cause was - but something you might want to look into.
Comodo Trust Logo
This requires a snippet of javascript in the header of your website for any page you wish to place the logo onto. I hate this requirement, but they write additional css includes and other items, so it must be there. I do not see this snippet on your site. For example if you were placing the logo on your shopping cart page you would create a new php file 'includes/templates/your_template_name/jscript/shopping_cart.php' (or just use 'includes/templates/your_template_name/jscript/jscript_comodo.php' for all pages). Inside this file put something like the following:
<script type="text/javascript">
//<![CDATA[
var cvc_loc0=(window.location.protocol == "https:")? "https://secure.comodo.net/trustlogo/javascript/trustlogo.js" :
"http://www.trustlogo.com/trustlogo/javascript/trustlogo.js";
document.writeln('<scr' + 'ipt language="JavaScript" src="'+cvc_loc0+'" type="text\/javascript">' + '<\/scr' + 'ipt>');
//]]>
</script>
