<asp:ScriptManager ID="ScriptManager1" runat="server">
<asp:ScriptReference Path="~/MyLocalScripts.js" />
<asp:ScriptReference Assembly="MyClasses" Name ="MyEmbeddedScripts.js" />
If you were worried about the SrciprManagerProxy object, they all work with it too. So you should have no problem with Master Pages. Also I believe you should be able to register your scripts at run-time too. When I get a chance I will go over that too.