Help with IE6

I am fairly new at websites, trying to make a site for my non-profit org (no $$ to hire a web guru).
I have created the following site and try to make it visible to IE 6 and later users but no luck.
The site is done with a few templates and I link the IE css in the head tag just like the other css. The templates are at the same level as my main pages but I then have many other pages buried lower than that. The pages on the same level seems to be displaying in IE 6 but not the ones buried lower. I also need help with the JS code for the dropdowns.
http://www.archbold-station.org/station
Thanks in advance

Don't know how to fix it though.
Here is the template code
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Archbold Biological Station | Conservation Biology | Lake Placid, Florida</title>
<link href="../assets/css/menu.css" rel="stylesheet" type="text/css" />
<link href="../assets/css/layouts.css" rel="stylesheet" type="text/css" />
<!--[if IE]>
<link rel="stylesheet" href="../assets/css/menu_ie.css" type="text/css" />
<![endif]-->
</head>
Now here is the code when I apply the template to a page
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Archbold Biological Station | Conservation Biology | Lake Placid, Florida</title>
<link href="../../assets/css/menu.css" rel="stylesheet" type="text/css" />
<link href="../../assets/css/layouts.css" rel="stylesheet" type="text/css" />
<!--[if IE]>
<link rel="stylesheet" href="../assets/css/menu_ie.css" type="text/css" />
<![endif]-->
</head>
notice the path statement changed for the two CSS but not for the one that's related to IE.

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