I've made a few Estes skyrockets (not too many though, the motors are very expensive!) and reading about my experiences should help you while making them.
The first Estes skyrocket I made used a D engine and a Class C aerial shell. It was launched from a 5ft long cardboard tube pointed straight up. It launched perfectly, going very high (as a D tends to do). After a short delay from the time fuse in the shell, there was a nice magenta burst high above. It was cool, but I think it went way too high. The sound was pretty quiet from the ground and the burst looked small because it was so high. I would not use D engines anymore for lifting any shell smaller than 2 inches.
Rocket with cob:
The next rocket I made was the above rocket, with a C6-3 and a cob payload, but was a bit nervous about it because I didn't know how it would fly with the (sort of) heavy payload. To test the design I made an identical rocket but filled the cob with water instead of powder for weight. The rocket flew perfectly, so I decided to launch the rocket with the explosive cob. The tube was angled about 80 degrees so it would hopefully go over an area that a) didn't have any houses and b) didn't have us directly below. It flew perfectly, the engine burnt out, then a delay, and the cob went. It was filled with paper match heads and the empty space then filled with whistle mix. This created a nice star-type effect from the burning match heads just before the sound got to us. The only thing I would have done differently would be a steeper angle.
One cob is good, two should be even better, right? That was the idea behind the next one. C's seemed to have enough thrust for it, so I attached two cobs filled with the same thing as the last one, with both fuses going into the motor to be ignited by a bit of powder I put in there. It was launched the same way as the last one. This time it didn't fly so well... It was clear the head was too heavy right away. The rocket tipped in flight after reaching less than half the altitude of the last one. I saw the ignition charge go off and then only one cob explode (at a fairly low altitude). This design proved to be unsafe, but a D size might be enough to get it to a safe altitude.
Double cob design without tape: