Concerning the fact that you don't see the good products, it's because you need to select the correct category as "parent category" in the hikashop options of your menu. You can access the hikashop options of your menus via the menu Display->Content menus in hikashop.
The menu is generated by your template, by something called mega menu. We can't help on that end as we don't know much about. You can find the documentation related to mega menu on that page:
wiki.joomlart.com/wiki/JA_Template_Framework/Navigation
Also, your template provider should be able to answer you.