I'm not much help on glove advice. I tried several different kinds out when I was younger, but by the end of a session, my hands were still pretty torn up inside. The best results I got were from doing a custom wrap on both hands, and using the split finger mma style grappling/striking gloves.
As for which knuckles to use... eh, it depends on who is doing the instruction. Top two, middle two, and bottom three are the choices here. The bottom three line up better with the forearm, without requiring the wrist to be bent at an angle during contact. I learned to turn the wrist slightly downwards prior to contact, and straighten into/through the blow. That, along with some simple waist twist and footwork action, can greatly increase the force delivered by your punch.
Supposedly, using the bottom three method increases the chance of fracturing the metacarpal behind the pinky, but that becomes less of an issue if you're conditioned for it. That said, I would suggest different punches for different targets. I used the bottom three method for most body blows, with the exception of muscle separation strikes, because it maximizes delivery and makes it very unlikely that I'll fold my wrist and take myself out of the fight with the first strike that connects. Against the front portion of the lower half of the face, I'd still go with the bottom three. It is generally a pretty good fit, and can easily act as a knock out under the correct conditions. The sides of the jaw, I'd use the top two for.
I should clarify at this point that I'm talking about vertical straight blasts as opposed to horizontal "normal" punches. Pinky side is down, thumb side is up. The only time I really use the "middle two" approach is in something like a normal hook, or if I'm punching around/over someone's guard, although I usually used a technique co-opted from Jiu Jitsu for that, which was still the "bottom three", only with the arm turned and the hook delivered as an overhand.
Against a target like the top half of the human head, where bones are stronger and there are plenty of surface abnormalities that can crush carpals thanks to a poorly made fist, I'd go with the "top two" approach, mostly just to concentrate the impact into a smaller area. This was also the punch I used for breaking boards or slabs.
Uechi Ryu has a great one knuckle punch (not to mention the toe kick) for muscle separations, but again, everything works better when you specifically condition for it.
For me, the best thing that helped me to minimize hand injury during training was learning to keep the fist tight during impact. I may only clench it a split second before contact, but I make sure it is a rock for its whole time on target. Gloves with the built in bar for you to wrap your fingers around can help.
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