I use both brakes for all stops or slowdowns, and the rear brake only for parking lots and trail (drag?) braking through low-speed turns to help on/off throttle control. As others have written, practice, muscle memory, etc. develops your skills that then will become more automatic in an emergency situation. And there is no debate about the fact that both brakes will stop you in a shorter distance then just the front brake alone. Even Keith Code makes this statement.
Hey, two friction patches will always add up to more then one friction patch alone.
One more way to consider rear brake usage - chassis stability. With most motorcycles (BMWs with the Telelever forks excepted), front brake only will compress the front suspension and extend the rear suspension. Rear brake only will compress the rear suspension with little effect on the front suspension. By applying both brakes, the rear of a motorcycle tends to lift less then under front brake only conditions. This results is less geometry change such as steering rake angle, less change in front/rear tire loading and other factors I can't quite define at the moment. Proper application of both brakes does make a significant difference in chassis stability. I have felt this with every motorcycle I have owned. As some previous folks have posted, the rear brake "loads" the rear suspension.
I adjust my rear brake pedal height to be fairly low (shifted by one spline notch and tweaked with the adjuster screw) which helps me in everyday rear brake usage. Also, I believe the trend with modern motorcycles has been to engineer less leverage in the rear brake system so that higher foot force is required. This, I believe, gives more feedback for control of the rear wheel and may help prevent accidental lock-up under panic conditions or by less rider experience. IMO, there is no question that the FZ6 rear brake, as on any well engineered motorcycle, is invaluable and absolutely essential for everyday riding.
Regarding comments that the FZ6 rear brake is weak. Quite the contrary, this brake can lock up the rear wheel at any speed, on any pavement, if so desired.