I use this type of code in my apps main xxxxxxxxxx.aspx page code-behind page.
Yes, I have a App_MasterPages folder with a layout.master file in my project folder, but it is just there as a place holder to allow compiling.
What I did have to do to get some Telerik code to work correctly with my app was to change my skin layout master as follows.
Here is the first 2 lines from my skins layout.master
<%@ Master Language="C#" AutoEventWireup="true" CodeBehind="~/App_MasterPages/layout.Master.cs"
Inherits="mojoPortal.Web.layout" %>
<%@ Register Assembly="Telerik.Web.UI" Namespace="Telerik.Web.UI" TagPrefix="telerik" %>
NOTE: The second line is Telerik.
Then in the same layout.master I needed to replace this...
<asp:ScriptManager ID="ScriptManager1" EnablePageMethods="true" runat="server" />
With this
<telerik:RadScriptManager ID="RadScriptManager1" runat="server" enablepartialrendering="true"
asyncpostbacktimeout="600" enablepagemethods="true">
<Scripts>
<asp:ScriptReference Assembly="Telerik.Web.UI" Name="Telerik.Web.UI.Common.Core.js" />
<asp:ScriptReference Assembly="Telerik.Web.UI" Name="Telerik.Web.UI.Common.jQuery.js" />
</Scripts>
</telerik:RadScriptManager>
<telerik:RadAjaxManager ID="RadAjaxManager1" runat="server" EnableAJAX="true">
</telerik:RadAjaxMana ger>
If you don't need RadAjaxManager you do not need the last 2 lines.
I only say this because you say you are using in-line scripts which would need a scriptmanager. If you are using scripts that are to work with Telerik controls you should use the Telerik script manager.
If you search the forums on "RadScriptManager1" you will find an old thread from 1.5 years ago where me and another developer figured this out.
There, now I have opened up a whole can of worms and you will regret I ever answered your post.
Arivixe.com
Rick