Sculpting Magnet fitting

I mostly just make the holes on one part and use them as guide for the second part. You can do this while the clay is still soft and just press the second part against the first and let the holes mark themselves. You could also rub a pencil on the edges of the hole and let that transfer when the parts are put together.

If you rather drill the holes after casting you only need to line up some kind of guide hole or spot to mark the center of the holes. You can probably get away with just mesureing it out.