As a follow-up, here's the code I used for testing:
Markup of the AsyncUpload, AjaxManager, and the drop zones:
<telerik:RadAjaxManagerrunat="server"ID="ajaxManager"OnAjaxRequest="ajaxManager_AjaxRequest"><AjaxSettings><telerik:AjaxSettingAjaxControlID="ajaxManager"><UpdatedControls><telerik:AjaxUpdatedControlControlID="asyncUpload" /></UpdatedControls></telerik:AjaxSetting></AjaxSettings></telerik:RadAjaxManager><telerik:RadAsyncUploadrunat="server"ID="asyncUpload"TargetFolder="~/Uploads"DropZones=".DropZone1,#DropZone2"OnClientFileDropped="onClientFileDropped"OnClientFileUploaded="onClientFileUploaded"></telerik:RadAsyncUpload><divclass="DropZone1"><p>Custom Drop Zone</p><p>Drop Files Here</p></div><divid="DropZone2"><p>Custom Drop Zone</p><p>Drop Files Here</p></div>