to answer your question how to plan what goes where i'll say don't worry about it too much. shrubs and understory plants are really flexible. if you think about the trees as the bones and plan for adequate spacing on those, the understory, shrubs, vines, etc can be cut down, moved, trimmed, pruned, etc if need be.
something i've also noticed in our 4 year old food forest is that plants will find the niches they like. we've planted dozens of indigo bush (Amorpha fruticosa) and in some spots they're leggier (more shade, poorer soil) than others, but it doesn't really matter. we chop and drop their foliage after they provide their abundant dazzling function as insectaries and trim them up how we like based on the other plants around them. vines also climb on them. furthermore, some patches of nettles, mints, medicines, etc do better than others. we have 4 different plantings of spearmint and a couple of them flourish while others are in shade and don't expand much.
i think it's cool to vary plantings and observe the habitats different things like. you can really get to know a plant when you see how it performs under all different types of conditions.