I use engine braking in addition to the front and rear brakes. I downshift, let out the clutch, and use the engine's resistance to slow the bike down, as well as both brakes. I almost never rely on the brakes by themselves (see next paragraph for urgent braking techniques). I also install a brake modulator on every bike I own: flashes once per second, for five seconds, then on steady, until I release the brake. It's much easier than trying to flash the brakes manually, which can jerk the bike by grabbing/releasing the brakes.
In an urgent stop, where I don't have time to slow down with the engine, I pull the clutch, and ride the brakes hard, downshifting as the bike slows -- I try to keep it in proper gear for the speed, as I'm slowing down, only shifting into 1st gear at the end, when the bike is at 10 MPH, or slower.
Try to always maintain the proper gear for your speed! If you have it in too high of a gear, the engine could stall, and die; if the bike is in too low of a gear for the speed traveled, the rear tire could slide out dumping you, and the bike.
Also,
always lead with the rear brake, applying it first, about 1/2-second before applying the front brake. This will prevent the nose from diving, stabilizing the bike's suspension, making stops easier, faster, and with better control. Practice in a parking lot, at low speeds, initially, to gain an understanding of how it works. It can be done at any speed, even in emergent braking situations -- this is where leading with the rear brake is even more critical to keep the bike's suspension stabilized. Cheers!
