I am just in the midst of playing around with this aspect and there seem to be a couple of different approaches.
First, forget about drawing your arcs to represent holes to start with. Just plot a point where you intend for the hole to be, and then get right in to the 2d surface tools or 3d solids functions.
In 2d, you can "create a surface" using circular plane and then create that surface to represent your 2d holes. It is quick and easy to select arc centers using your existing points.
But why even bother, just go straight into 3d solid, and create a cylinder immediately on those same points. Then, just use the solid cutter to cut the holes from the existing surface. Don't forget to blank or delete the "plugs" from the holes or it will still look filled in when you render it.