When it comes to making punch marks I relay on two types of punches. If I layout my hole locations and need to mark the starting point I will use an automatic punch. An automatic punch looks like a regular center punch. The only difference is that you do not strike the back end of it with a hammer. Instead you push down on the back end till the punch "automatically" punches the material. How? As you compress the punch you load up a spring. At the end of the stroke the stored energy is suddenly released against the punching ram and it strikes the object. Though the strength of the punch is adjustable, I find that these punch marks are on the light side. Some of the reasons to use such a punch is less tools required, better accuracy placing the punch, and single handed operation. Once established, a light dimple can be made deeper with more hits from the automatic or with a regular punch and hammer.
Sometimes a situation arise and you need to transfer a series of holes from a part onto the surface to another. Examples are ski bindings that need mounting or a bracket that you need to pre-drill holes for. The tricky part here is the the center punch is too wide to fit in the hole to make the transfer, or that it will be difficult to determine the center of the hole to be transfer with a standard punch. The solution is a transfer punch set.
Transfer Punches come in a set with many varying diameters of punches. You find the punch that fits the hole best and use it to mark your work piece. Since drill bits come in many different series of sizes (letters, numbers, fractional, metric), a typical hole can be of any size. Transfer punch typically only come in fractional sizes (fraction of an inch). The fit is never perfect but good enough. Transfer punches are not of the automatic variety and thus a hammer is needed to deliver the dimple making blow.
When creating a set of holes never transfer all the holes at once. What I mean by this is do not lay the part down on the work piece, dimple mark all the holes then drill them all out. Instead I typically transfer one hole. Bolt the part down with the one hole, then transfer the next. If the part has more than two hole, I will do the first two holes individually then do the rest at once. Once two of the holes are fixed, there is no chance of that part rotating, and you have a equal chance all the rest of the holes will then line up. I find that this is a much more accurate method of transferring a set of holes.
And there you have it, another chapter in the life of drilling holes. (said with a southern draw, like an instructor I once had did, makes that last sentence funnier)