Bookmarks created in a document are tied with the same document using .shared file.
If I understand it correct, Main_Application is also a distributed application and the other Appliction1, Application2, Application3.... are kind of subset of Main_Application.
So, if a user creates a bookmark in Main_Application, those will reside in Main_Application.qvw.shared file.
if you want these bookmarks to be available in all the other documents as well, you should manually copy Main_Application.qvw.shared file and rename it as Appliction1.qvw.shared, Application2.qvw.shared etc.
The catch here is its a one time activity.
Once you copy and replace the shared file to the other distributed documents, all the existing bookmarks will be lost.
New bookmarks created in Main_Application.qvw are not automatically transferable.