First, you must realize that markup information is not placed directly into the document file. Instead, it is added to the "view" by SwiftView. How does SwiftView know what markups to display?  Markup information is passed to SwiftView via ICS (image command set) markup commands. 

You could create an ICS file for every document that requires markups.  In the following examples, instead of connecting directly to the named file, the hyperlink connects to an ICS file.  The ICS file contains an "ldoc" command whose argument is a URL to the actual document ("1page.hpg" or "2pages.hpg").  Additionally, each ICS file contain the markup commands.  1page.hpg will display the markup string "STATUS: NOT Released", while 2pages.hpg will display "STATUS: Released to Manufacturing".  The date and time of the document are also displayed.  These strings are displayed on what appears to be "yellow sticky notes".
    [ 1page.hpg, 2pages.hpg ] [ View Source: markup1.ics, markup2.ics ]

In this second example, we use a more generalized approach.  The ICS commands are generated by PHP3 (a server-side HTML-embedded scripting language) embedded in our file markup3.htm.  ICS commands can be generated with ASP, CGI, or JSP as well.  An ASP file that does virtually the same thing as our embedded PHP3 can be seen here.  In our PHP3 code, you'll see that the file name will determine the markup string, because markup files are associated with a particular document.  Should your application include a backend database, your PHP3 (ASP, JSP, etc.) could obtain the markup information as well as the associated document from your database.
    [ 1page.hpg, 2pages.hpg ] [ View Source: markup3.htm ]