Just place the content placeholder in the section of the main chapter, and then write the scripts related to the site with the asp: Content tags of your pages.
Master
<%@ Master Language="C#" %> <html> <head> <script type="text/javascript" src="scripts/jquery-1.4.3.js"></script> <asp:contentplaceholder id="LocalScripts" runat="server" /> </head> <body> </body> </html>
Page
<%@ Page Language="C#" MasterPageFile="~/Master1.master" AutoEventWireup="true" Title="MyTitle" %> <asp:Content ID="Content1" Runat="Server" ContentPlaceHolderID="LocalScripts" > <script type="text/javascript"> $(document).ready(function () { </script> </asp:Content>
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