Ah ok, I think I understand what you're talking about now.
The sub category displayed in the category listing of the main area is displayed because of the option "Show sub categories" of your menu. If you set it to "no child", you won't see it anymore.
The menu position option that you see in the configuration is for the menu of the backend. It's the one you see below the title of the page: System | Customers | Orders | Help
So changing that won't affect menu items on your front end in any way.
Regarding the development of payment plugins, we know a few developers who can do that. For example you can contact brainforge on our forum via private message:
www.hikashop.com/en/forum/profile/userid-423.html
He already built several payment plugins for HikaShop.