Shaning,
- Right click the popups folder in flash builder for your Flex Viewer project and choose new > File and name it PopUp_???.xml Then copy and paste the text from one of the existing PopUp.xml files and modify it for your needs.
- As mention in answer one you create it in the popups folder.
Of course I don't see what any of this has to do with sub layers appearing in the LayerList widget though. All this will do is allow you to specify popups for individual sublayers of a dynamic or tiled map service.Don't forget to click the Mark as answer check on this post and to click the top arrow (promote).Follow the steps as shown in the below graphic: