I would want stalls of some sort. Maybe figure our how many horses are going to be in a pasture and build the run in on the fence line closest to the arena with stalls and access from both sides. (pasture side left open all the time unless horse needs to be contained, outside world side always closed) then you build your paddocks in an arc or square around the arena and other facilities.
I think the term pasture board has already been mentioned so no need to cover that.
I don't know how familiar you are with pasture rotation, but I have seen it done very effectively with a large variety of livestock. The farm I worked at didn't have horses, but after the sheep were rotated through a section of pasture next went a flock of chickens then the cows and then another flock of chickens. The chickens would eat the parasites and spread around the cow pies. The farm was well balanced so that they never mowed but never had a shortage of good grass. Every once in a while the fields would get mowed in the fall just to level everything out. They would rotate the section of the pasture was left for hay every year as well. They would compost and had a veggie garden that was split in half with a fence down the middle veggies on one side and compost with another flock of chickens on the other. They would flip flop the chickens and the garden every year.
Anyway, back from my tangent, if you are serious about the natural part and are doing pasture board think heavily about pasture management and the capacity of the land you use. Can the land seriously be expected to sustain the number of horses? If not then you need to reduce the number of horses or supplement their diet. Really think out the design of your facility design it to be low maintenance / maintains itself.