First, I don't think there's any restrictions on using Helvetica Neue so feel free to use that in you app for whatever you need.
San Francisco font doesn't show up when enumerating installed fonts so you can't "pick" it in the usual sense. If you use the UIFont systemFont APIs, and San Francisco is the system font, it will be used automatically and you don't need to install anything. In fact, Apple prohibits installing SF font in your app.
And if the system font is Helvetica Neue (which was standard before SF font), you will get that automatically by using systemFont APIs. So that's the correct way to handle this situation. systemFont will pick Helvetica Neue when it is system font on old systems, and SF on newer systems.
Doug Hill
https://github.com/djfitz/SFFontFeatures/graphs/traffic