DO NOT drill the holes separatly, when you assemble it will not line up. Funny because I taught basic hand sewing this morning and the same issue came up.
Mark your holes, glue your pieces togeather then poke your holes. To drill the holes use a large sewing machine needle (tandy sells them) in a dremel. It will drill good holes, it does not remove leather like a drill does and it is fast and easy.
Aaron