Karate style punches were created to penetrate the wooden armor of the Bushi (only the Samurai officers could afford metal armor). If punched with the first two knuckles, the wood broke and the broken ends would possibly stick into the soldier. This first two knuckle style punch is the one used in Taekwondo. Some think the impact area should be the last three knuckles. In this position, the top of the fist is not parallel to the floor but angled downward about 45 degrees toward the little finger. Is debatable which way is best, so the method you are taught by your instructor. If you practice both ways, when you are suddenly attacked on the street, you will end up using something in between the two that is ineffective.
Old bare-knuckle boxers rubbed sheep urine and alum crystals into their hands after punching practice. A better substitute is mentholated spirits. After punching only a fairly rough surface, such as a heavy canvas punching bag, the knuckles will be reddened. Then rub in the spirits and let it dry. It takes about a month of three or four times a week, and your hands get quite tough.
When punching start with the fist relaxed and just before impact squeeze the fist tight. Practice punching from a normal stance as you would have on a daily basis. From this position, suddenly punch the target, coordinating everything to get maximum power.