MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
5mm x 2mm disc magnets should work, but wouldn't be flush. Which might work fine. In my testing there wasn't much difference between the magnets flush or protruding a little, but having them flush made for a more consistent fit for the adapter lens case.
The curve of the headset lenses means that the center of the lens is above the rim of the magnetic base, so it might not work great as a glasses protector. I'm on a trip, but I will take another look at it in a week or so and at the very least could make a version that accepts a 5mmx2mm magnet.