Nina, I think the ones I used were about 1" or a little larger. That way I could use my Martha Stewart 1" circle punch to punch out the paper for the bottom.
I found a few of my smaller stamps that would work on a 1" circle. I will say it turned out to be more of a project than I imagined when I started. They turned out cute, and I gave sets of them in little metal tins for Christmas gifts.
I had the best luck with using E6000 adhesive for both the circle and the circle magnets. It works well, but the fumes are something else. I think I found the circle magnets at Hobby Lobby, too.
Here is a really good photo tutorial:
Coconut Love: Super Easy DIY Glass Marble Magnets