This is a great question because not only are there ways they can work together, there are also ways in which they won't work at all. The fact that they are physically identical can also lead to a fair amount of confusion!
Here are the hard and fast rules about the two technologies:
- You can use a USB-C device with a Thunderbolt 3 port
- You cannot use a Thunderbolt 3 device with a USB-C port
That is the easiest way to approach it. For most users, an issue with this will be almost non-existent. For some, specifically power users and early adopters of the Thunderbolt 3 technology, it can lead to a headache.
As long as you know what type of technology your peripheral uses and what type the port is you will be plugging it into, you are ahead of the game.
Thunderbolt 3 has quadruple the bandwidth of the latest version of USB (3.1). This lets you do more with a single port. Charge and sync multiple devices simultaneously and rapidly. For those that need the speed that it offers, and don't mind the premium, Thunderbolt 3 is the way to go.