I also thing side by side. That way there won't be roosting in front of the top one, which is over the opening for the bottom one. I recall my mom saying the chickens she had as a kid squabbled over the perching spot for the top box because it was recessed back a bit, like you have yours. I don't know if the lip will hold a big girl to land on and jump off from, from the picture, if you were to have the fronts at the same depth. Having them closer together and side by side isn't a problem, if space is the concern.