Engine braking is fine, but you should also flash your brake light to indicate your deceleration to the cars behind you.
This is done by gently pulling the front brake lever in and out a few times; just enough to engage the brake light switch, but not enough to engage the brakes (unless of course you need or want to brake).
If you are already stopped at a traffic light, it’s also good practice to check your mirror and flash the brake lights (followed by a steady brake light) to attract the attention of the driver closing in on you from behind.
You can also buy accessory automatic brake light flashers (not legal in all states) and/or accessory light-bars which connect to your tail and brake light wiring and will flash when the brake light comes on. These are legal I believe, as your main brake light remains steady.
You can also use hand signals to indicate deceleration, but that gets old soon and isn’t always possible.