[Stiglr]

When forced to create an aperture in a polygon manually (and it's often well worth it, because Booleans usually create a horrible mess!), I often use this tactic:

1) Reduce/simplify the polygon to a single surface.
2) Select the surface in Surface Selection Mode.
3) Surface > Make Hole. Insert or delete vertices among the hole vertices such that the hole has the same number of vertices as you want the hole "cylinder" to have.
4) Create a disk object, with the same number of segments that you want your hole to have. Size/scale the disc to the size of the hole.
5) Drag the disk over the polygon, position and then "Lock:" it so it is visible but non-selectable.
7) In Vertice Select Mode, select the vertices that comprise the inside of the hole you created in the polygon. Drag these directly over the vertice points of your hole polygon.

Basically, you're "tracing" the hole, using the disk object as a positioning guide.