If you are trying to include a javascript or css include into the page template, you can directly edit the site.master file that lives inside the folder for the theme you use. So for instance if your theme is called MyTheme, then you can edit /themes/MyThemes/site.master.
You can also use a little ASP.Net code like this to make the path portable rather than relative to the root of the domain:
<script src='<%# ResolveUrl("~/themes/MyTheme/jquery-1.2.6.pack.js") %>' type="text/javascript"></script>
Also notice that if you have <head runat="server">
inside your site.master file, then css link tags will resolve out correctly, relative to the site.master file, so you don't have to write any special code to make the path protable like the script tag example above.
<link rel="stylesheet" href="master.css" type="text/css" />