You can easily place markers inside PDF using HTML links like this:
Link to the area with that marker:
<a href="#marker1">jump to Marker1</a>
Example input HTML:
Navigation: <a href='#section1">Section 1</a> | <a href='#section1">Section 2</a> .... <a name="section1"></a> <h1>Section 1</h1> ... ... <a name="section2"></a> <h2>Section 2</h1> .... ....
Output PDF will have these links and use will be able to click on the links to jump into specific pages / areas similar to the original HTML.