By default the <ext:ScriptManager> will add the required <script> includes as the last items within the Page <head> section. You can control the exact placement of the required resource files by adding a <ext:ScriptContainer> to any specific location with the <head>.
The <ext:ScriptContainer> may be required if you have separate JavaScript includes or blocks or inline JavaScript which need to execute "after" the Toolkit resources are loaded.
The following demonstrates adding an <ext:ScriptContainer> within the <head>.
Example
<head runat="server">
<title>Untitled Page</title>
<!-- Add ScriptContainer to customize location of required Toolkit resources (js & css) -->
<ext:ScriptContainer ID="ScriptContainer1" runat="server" />
<!-- Add custom JavaScript after ScriptContainer -->
<script type="text/javascript" src="../js/custom.js"></script>
</head>
Hope this helps.