humbledesigner,
There are a few ways:
You may create all the punch through paths with a black stroke and no fill, then then Group them and:
A1) Object>Path>Outline Stroke, ;
A2) Also select the path to be punched through and Pathfinder>Minus Front.
B) Also select the path to be punched through and in the Transparency flyout click Make Opacity Mask with both Clip and Invert Mask unticked.
B) will allow you to Release Opacity Mask and edit the punch through paths free, then reapply.