placing and referencing .css files, and javascript files in the production server

I am using asp.net 2005 - 
In my hosted server (provided by third party company), I upload my files and sobfolders.
One of the sub folder contains .css files, and javascript files.
My question? how can I refer these .css files and  javascript files from the  markup?
I am using master-detail designing, where to place these reference in masterpage or details page?
should the reference to be made from <Head> only?

 see my current reference
<script src="<%= Request.ApplicationPath %>/SUBFOLDER/javaScriptCM.js" language="javascript" type="text/javascript"/>
<link href="<%= Request.ApplicationPath %>/supportfs/StyleSheet.css" rel="stylesheet" type="text/css"/> 
thanks in advance

 
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