Fabric yo-yo's are usually sewn together with the "hole" side up. They have traditionally been made into coverlets that go over the top of a plain bed spread. Now they are being sewn together to make wall hangings, sewn on head bands, used on necklaces, as flowers on appliqued stems and more. If you "google" quilt yo yos you will find a lot of ideas.
If you don't mind reading below, I gave a pretty good answer. The yo yo's are laid out first and then usually stitched by hand at the sides. When the rows are put together, then the yo-yo's are stitched together at the top and bottom. A picture is worth a thousand words here, so google quilt yo-yo's and it will make more sense than what I just wrote!!!