There are some rules of thumb.
Large areas are known to need cropland, cities, industry, transportation hubs, military bases, navigatoinal aids, and wilderness. The trick is to get the greatest value of assets over time.
First, don't build on flood plains or earthquake faults. These are best kept for parks, or perhaps unimproved farmland. In any case, limit capital improvements. Some of the most beautiful cities, such as San Antonio, use this principle.
Build on hills and ridges. This keeps buildings off flood-plains, and away from filth borne on water and insects. It also reserves the fertile flatlands for farmland and assures cooler homes in summer and warmer, solar-heated ones in winter.
Build transportation corridors first, and make them form hubs and spokes. Development will follow. Since we want cities on hills and ridges, then hubs should be atop of hills, and roads should follow ridgelines.
Standardize on a simple, flexible transportation system like busses, and then make it as efficient as possible, with innovations to get passengers on and off quickly.
Make the administrative and transportation hubs the same places. In that way, the networks for administration can use the same capital improvements as the transportation networks. This means hubs will be atop hills.
In general, plant so as to produce the greatest value with the least work. That is, if orchards give the best return per man-hour, plant them.
Designate locations for nuisances. Then assure that all nearby persons contract to let nuisances be built there.
In general, every square mile should be self-sufficient in food, water, transportation, communication and fuel, well-enough to prevent starvation, dehydration and freezing. Buildings can have solar heat, solar cells, wind-power, cisterns, and vegetable gardens in roofs, if it's a priority.
Let every area serve also as wilderness. Provide incentives and space for wildllife migration grids and greenbelts. Grow meadows on roofs, roads and parking lots. Place nesting sites on buildings. Use ponds for air-conditioning heat-sinks, storm swales, and riparian wildlife.
Make every area serve several purposes. For example, let parks consist of gardens, unbuildable zones, and edible plants, harvested to market.
Avoid social institutions that stratify a region by income. For example, encourage school vouchers so that rich people don't have to pick schools by buying houses.
When designing cities, set up a cellular structure that combines housing, parks, crops, greenbelt, drainage swales, throughways, local streets, parking and shops. Repeat the cells, and include mildly different road furniture and a distinct ornament or shop at each gate or crossroad.
Consider building codes that make best use of the land.
Consider building codes that make a building more defensible in war-time.