I'm not sure what you are asking here. Are you trying to take a set of HTML pages and make them into a desktop application?
This is what I learnt. It is possible to get the HTML files to look like regular Help with a left pane and so on using Adobe AIR. I created HTML files using Amaya ver 11.3.
Please suggest as to how I should go about it.
Create an application descriptor that references the index or main HTML file. Run the ADL utility to test it. Use the ADT utility to package things up into an AIR file.