Adding JavaHelp topics to a NetBeans Platform application is made really easy by the NetBeans IDE. Run the New File wizard, and choose the Module Development category, and under File Types pick JavaHelp Help Set. The wizard will generate all the necessary files for you.
The one thing in the process that was not obvious to me when I did this recently, is how you change the order in which help topics appear in the final product. It is in fact also very easy once you know how.
Open the generated package-info.java file, and have a look at the @HelpSetRegistration annotation. You will notice that it has a position attribute. And changing the position of the set in the final product is as simple as changing that value!