By you question I guess that you users are not logging on to an application set in Program Neighborhood. If they do that then you can configure the publsihed app on the server to put an icon on the users desktop or in the start menu. Another solution would be to create an ica-file for the app. You do this by right-clicking on the published app on the server, in Publsihed Application Manager or in the CMC depending on which MetaFrame version you are running, and then choose "Create ICA-file" and follow the instructions. When you have an ICA-file that works the way you want, window size and so on, just distribute the file to the users desktop.
Hope this helps
/Hof