Rebekah, I wish I could give you some good info on breaking them in. I just do what I do with all my boots and shoes - wear them around the house for a while just to make sure they'll be tolerable on my feet, and then gradually put them through more paces to break them in with everyday wear. Although I jumped right in and wore these for a full day, including 4+ miles of walking! My feet were tired by the end of the day, but certainly nothing that wouldn't be unusual for wearing many other shoes for that much walking.
I wonder if a leather cream might help -- something that softens and conditions the leather just a bit to offset any stiffness in the uppers. You might want to give that a try if your boots feel stiff on your feet. I've done that with a stiff leather jacket and it did help.