I use a wing divider to mark the stitching line first. Then I take my pricking iron, put it on to of the line, and then make sure that the iron is standing straight before I punch it through with a mallet. What you can do is get a piece of metal, have it bent in a vice to 90 degrees, to be sure that it is at a perfect angle to your stitching line when you lean the iron up against it.
As for the noise, I use my granite slab then topped with one of my smaller self healing cutting mats and then my poly punch board. Sometimes I even have a thick piece of scrap leather on top of the poly board to save the points of my pricking irons. All this is killing the noise besides the whacking on the iron. However, there is another solution that is very quiet, and that is getting a set of pricking pliers. These work in the same way as with a pricking iron, just with the teeth set on a set of pliers so you make the holes by squeezing instead of punching.
https://www.youtube.com/watch?v=HgNaR_Sz6rU
Hope this helps,
C.