Barb, there are two approaches to this. One, the viewing window is an IE browser pane. It will render html and if you have an activeX plugin viewer for a given file type then you can set that as the default viewer and it will appear in AC. Try to set pdf Annotator as the default, show-in-ie plugin.
Two, you can just set it as the default .pdf viewer, then when the doc wants to edit they right click, then select view in default application. It will open in .pdf Annotator.
HTH, always glad when I might be of help.
