There are two ways:
1. Press and hold the HOME key with the remote facing the FireTV box and observe how the white indicator light blinks. You will notice it blinking slowly and then a little faster...that means it was trying to pair the remote and paired it. You will also get a notification on the screen (bottom right).
2. Download the FireTV remote app. You can pair it two ways - One by having both your mobile device and the FireTV box in the same network or by signing on your remote to your Amazon account (which the FireTV is configured with). Strangely, the app in the iPhone SE wouldn't let me signin, the signin button to the lower bottom of the screen is not clickable!!!!! I used an Android phone and it worked like a charm.