In a small saute pan, warm the oil and then add the diced onions.
Cook over medium heat, stirring occasionally for 15-20 minutes to caramelize the onions. You can cook them longer for a more intense flavour.
Remove from heat, stir in the poppy seeds and season with salt and pepper to taste.
To shape the dough, make a small depression in the center of each dough ball with your finger. Expand the well by gently stretching the dough, working from the center toward the edges. The depressions will puff back up slightly while they bake, so make the well a bit more pronounced than you want it to end up; about 2-3 inches in diameter. In terms of depth, the dough at the bottom of the depression should be relatively thin; about ¼ inch thick. The bialy should be about 4-5 inches in diameter.
Fill each formed bialy with about ½ tablespoon of the filling mixture and sprinkle lightly with additional poppy seeds.
Place a pizza stone a in your oven’s center rack. Then, preheat oven to 475°F.
When preheated, carefully transfer the filled bialys to the pizza stone using a parchment-lined pizza peel or rimless cookie sheet. Bake for 8-12 minutes until the bialys are lightly brown. Remove and let cool on a wire rack.