For the marking of each document to each user you would need another table that is basically a Join table between users and documents. It is basically a many to many relationship. You would need to have the userID, the documentID and possibly a date field to show when the document was viewed.
As to the opening of the documents - I have found it difficult to be able to open documents on the server from Filemaker directly. The best work around I have found was to have the document (stored as reference) in a container field, then set up a button to export the container to the users temporary file path with the open after export option checked. That way even though the file is actually copied to the user's computer, it is stored in the Temp folder and deleted at some point by their system. This prevents users from actually altering the source file in the library (at least when going through Filemaker) which in our case was desirable.
Mark, that's great- both parts of your answer appear to be purely excellent! I think that should absolutely address my question. Thanks very much!