Note that using both RadAjaxManager and RadAjaxPanel for updating the same part of the page is not a supported scenarios as this may lead to rendering of nested UpdatePanels on the page. There are a lot of issues that may appear when using both the manager and the panel in some complex applications - MasterPage or WebUserControls. However, note that a single RadAjaxManager (and no panels) and in the master/main page and RadAjaxManagerProxy control could handle all the scenarios.
The RadAjaxPanel functionality can be simulated completely by the manager - simply replace the RadAjaxPanel with an ASP:Panel. and add those asp Panel controls to update itself in the RadAjaxManager settings.
In case you are referring the RadAjaxPanel into some client code you should revise your logic and in case manual ajaxRequest should be invoked you could use the RadAjaxManager for the same purpose.
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