What I do when I need the holes exactly cventered, is to make an exect copy of the item out of "Poster Board". Mark where the holes have to be, then punch holes in the poster board larger than what is needed. Then using a GEL pen, I will mark the holes while the template is laying on top of the item. By making round marks, you wil be able to line the punch's outer edge with the marks, and punch perfectly.
When purchasing the GEL pen, be sure to take a piece of leather with you, and be sure that it is one that will just rub off of leather once written on it. There are some that will not clean off easily, and others that will just wpie right off leaving no trace at all.
Hope this helps
Ken