All pads bed-in differently.
What I do is start out out full stops from about 30 mph. The trick is once you start you continually add pressure on the lever until you stop, don't release and add pressure again (pump the brakes). Do this 5-10 from 30 mph then increase your speed to 45mph and do another 5 stops. The pad will have a good start on them, just practice smooth consistantly increasing pressure on stops for the first 100 miles or so, try not to pump the brakes until they are bed-in.
You will notice your rotors will have different wear patterns, this is normal. The new pads are wearing down the rotor and adding in material. A good idea is to rub your rotors down with a green scotch-brite pad before you put on new pads. What you are doing during bed-in is that you are adding brake pad material on the rotors.
It is also a good idea to scrub around the base of the caliper piston BEFORE you put in new pads. You will have to push the piston back into it's bore and there will be alot of dirt on the exposed part of the piston. If you don't clean it up good before pressing it back in, that dirt may make it past the seals and into the bore...and then into your braking system.
It sounds like you are hearing normal bedding-in noises. If it keeps up past 100 miles, I would start to look at the calipers themselves.