On the main page, you can add more content holders that your content pages can fill with their own jQuery
So, at the head of your main page, do something like:
<asp:ContentPlaceHolder ID="Javascript" runat="server" />
Then on your screen browse the pages
<asp:Content ID="Content1" ContentPlaceHolderID="Javsacript" runat="server"> //js here </asp:Content>
However, you might consider including your javsascript in separate JS files and including them in order to relate your problems a bit.
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