Note that the in order to have the RadAjax components works correctly on the page you should use RadScriptManager instead of the ToolkitScriptManager.
As for the user controls ajaxification as you mentioned you should place the RadAjaxManager on the MasterPage.
Depends on the controls you need to ajaxify there could be a RadAjaxManagerProxy on the content page and ajaxify the whole UserControls there, which will force all controls in the ascx files to perform ajax.
Another possibility is to avoid the usage of RadAjaxManagerProxy and add programmatic settings in the userControls you need for the specific components you need by getting reference to the main RadAjaxManager. This could be easily done by using the RadAjaxManager.GetCurrent() method to access the manager and apply the needed settings programmatically as described here
You could also review the following online resources which elaborates on similar scenarios:
the Telerik team
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