Indeed with RadAjaxManager for ASP.NET AJAX you can only have a single manager on a page/master page to ajaxify all controls within the same page/content pages. However, if you define the ajax settings programmatically within the composite control to refresh only certain controls when a specific action is triggered, only the marked controls will be updated when the ajax request is executed. Hence you can still define granular ajax settings inside your composite controls.
Further information about how to perform ajax updates inside composite controls you can gather from this resource
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