I used to teach the braking class for one of the largest trackday providers in Northern California. Here's a condensed version of what we used to tell novice students:
1) Shifting is about putting the bike in the right gear for the speed you're traveling and keeping it there. Because braking changes your speed, you'll often need to shift around the same time that you're braking, but it's best to think of shifting and braking as two completely different skills
2) If you want to change the speed of a motorcycle drastically, you must use the brakes. Don't worry about engine braking unless it's upsetting the chassis or you're racing and looking for an extra tenth or two per lap.
3) All motorcycles generate the most braking power from the front brake. For many motorcycles, the front brake is the only one you need to worry about. If your bike is long and heavy (think: cruisers, touring bikes) you may also want to use the rear brake. If you ride a sportbike, standard, or naked bike you should probably concentrate on the front brake. I've run enough parking lot braking drills to know that it takes a very skilled sportbike rider to brake shorter using both brakes than when using the front brake alone.
4) Proper braking technique is to squeeze the tank with your knees, pull the front lever quickly but smoothly, wait until weight transfers to the front wheel, then increase lever pressure until you're generating maximum braking (but not locking the front wheel). The key here is you must wait for weight to transfer to the front wheel if you want to get the maximum amount of braking. If you grab a handful of brake before weight has transferred to the front, you risk locking the front wheel.
Proper braking technique would change slightly if: you're riding in the rain, you're looking for maximum lap time, or you ride a bike with a top-tier ABS system.