Only use theme-menu on part of site

Im using a help authoring tool(help & manual) that generates a HTML-site/manual with a fairly complex structure (CSS, javascripts, table of content sections, meta data etc).

Now im building a wp site, and i want a header/navigation bar that includes a link to the manual. When clicking the link i want the navigation bar to stay the same, and “push down” the contents of the manual, without interfering with its looks and structure otherwise.

How should i go about this the simplest way? Im new to wp and not a coder, but im not really in a hurry. The manual gets updated pretty often so i want a solution that doesnt require to much work everytime i want to make small changes.

Any help will be appreciated.