The "nesting box" needs to be a safe, clean, warm, dry place for kittens to get the tremendous amount of sleep they need to grow and develop in the critical first few weeks.
The nest box does not have to be elaborate, and using a cardboard box works just fine!! Warmth is going to be especially vital in the first two weeks of a kitten's life, as they are not able to shiver, and you cannot tell when they are cold.
When using the heating pad, be sure to keep it on the lowest setting, and wrap it well with towels and waterproof pads. Set the heating pad BELOW the box itself, to one side or corner under the nest box, so that the kittens can move to a cooler area inside their box if it becomes too warm for them.
You will want the nest box to be in a quiet, private, draft-free location, with the sides of the box high enough to keep the kittens in, and the overall box size large enough to allow for some exercise.
Be sure that the kittens can not get stuck under some pads in the sides or corners of the box, or that they cannot climb under the layers of towels and get directly on to the heating pad (which is why I recommend placing the pad itself under, not in, the box).