There are two things at work here. There's harmonics, where you're working with a relationship between two or more frequencies; and then there's the absolute frequency, which is needed to get different instruments to harmonize. Tuning forks give you an absolute frequency.
Harmonics are how you figure other notes are in tune with your absolute note - they're related to how the frequencies interfere. But that only tells you how to tune one note relative to another. It doesn't help you get a bunch of instruments in tune with one another, even if they're in different locations, etc.
Perhaps if you explained your confusion more, it could be answered better.