Todd,
I believe this is a terminology issue. When you say you have built several FlexViewer2.0 sites already do you mean that you have added the FlexViewer 2.0 Source code to FlashBuilder as a project or just changed the xml configuration files to suit your needs? If you have only been configuring the xml files then you likely have not down loaded the FlexViewer 2.0 source code which would contain the MapManager.mxml.