Stuffings, liners, deadeners, diameter and length of ports all affect how sound is produced. While theories exists, it's really tuning by ear.
The main tuning is by design. Box internal volume, structure, port dimensions if any.
In my case I talked with full range guru Bob Brines of Fostex MLTL fame. He suggested this box. 5 liters, tuned to 100hz. The smoothens the midrange up. I built it to the letter and the result is fantastic.