To make the onion filling:
In a large saute pan, cook the onions with salt in 2 tablespoons olive oil over medium-low heat until very soft and caramelized, about 30 minutes. Add the minced garlic and thyme and cook for an additional 5 minutes. Season the onions with salt, and pepper, to taste. Cook's Note: Slightly under salt to account for the salt from the anchovies and olives.
Preheat the oven to 425 degrees F.
Stretch the dough into a long rectangle and place on a greased baking sheet. It should almost fit the size of the baking sheet. Spread the onion mixture on the dough, leaving a small border. Arrange the anchovies and olives decoratively over the onions. Brush the exposed dough with the remaining olive oil and bake in the hot oven until golden and cooked through, 15 to 20 minutes.