This has worked well for me. I do it all at once, in a huge parking lot or empty freeway.
Step 1- Do a series of 5 back to back normal to moderately aggressive stops from 40mph to a rolling stop. Do not come to a complete stop, but almost. Do not ride the brakes during the break in process.
Step 2- After the first 5 stops; drive around at normal speeds for approximately 10-15 minutes to cool down the pads. During this time, try to use the brakes as little as possible. If you have to stop, do so moderately and then use the parking brake to hold yourself in place until such a time that you can proceed with the cool down. The object is to keep from imprinting a layer of friction material onto the hot rotor.
Step 3- Repeat Step 1 and 2 again.
Step 4- By this time, the brakes should be safe enough to drive normally and should be left to cool down overnight if possible.
Step 5- After an overnight cool down, repeat Step 1 and 2 again.
After Step 5, drive and use the brakes normally. The stopping performance should continue to improve steadily until it finally levels off.