Hello Akshay,
in this cases we usually recommend that you look for a similar existing component in the Mobile app, and use it as a base to develop your own. The problem here is that we don't have any component/addon similar to a payment gateway.
Where to place the plugin depends on where are you going to show it in the app. If it's going to be a new option in the side menu or in a course (like participants and so), you should create a new "addon" in the www/addons folder. If you want something unique you might have to put your code inside the affected component in core/components.
About the architecture, you should check any of the addons in the app to see how it goes. It follows Angular's architecture: controller, service, template, ...
The app uses the functions $mmSite.read and $mmSite.write to call WebServices, depending on if you want to cache the result or not.
I suggest you to look at this page to know more about the app's architecture. Also, this page might help you too.
Good luck!