baked whole wheat chocolate chip cookie bars stacked together

It’s really quite simple, actually. If you want thicker, taller bars or brownies, bake them in a smaller pan. Many recipes that use a 9×13-inch pan can be made in an 9-inch square pan just fine; and many recipes that use a 9-inch pan can be made in an 8-inch pan (of course, there may be exceptions).

You’ll need to adjust the baking time as thicker bars will take longer to bake, but you shouldn’t need to make any other changes to the recipe.