The key difference between laboratory scientists and the rest of us is that they have the luxury of closely examining one particular topic in isolation from other influences.
No businessman or farmer can do that. In fact, no engineer or any other manager of any system outside the laboratory can do that.
What the lab scientist does is reductionistic. What the businessman, engineer or farmer does is holistic. We have to juggle multiple variables and multiple goals to make the whole system work. They isolate single variables to try to understand why the system works.
In American agriculture we have applied reductionistic scientific methods extremely well. The result has been high levels of production of raw commodities.
But we have not understood or applied holistic methods very well. And the result has been and is again crisis in rural areas.
A skill basic to holistic decision-making is synthesis and integrative thinking. A number of holistic decision-making methods have been developed which use these skills and work well at helping folks like you manage agroecosystems. The most effective are shown in the graphic and links below.

A widely popular Australian holistic management program is property management planning. This national effort has been adopted by each Australian state.
It is similar to holistic resource management in the U.S.
A variety of American resources are available to help you learn holistic approches to management: Defining holistic decision making--as simply action based on a recognition that wholes are greater than, and something different from, the sum of their parts-- one out of the Northwest focuses on paradigms and decision-making frameworks--understanding some of the paradigms and beliefs that influence the way we make decisions in agriculture, forestry, government, business, the nonprofit sector, and private life.
Becoming adept at holistic decision-making is just one aspect of learning to transform systems. Look into the other areas:
The quickest way to develop skills in systems facilitation is to find someone who is successful in helping groups create new systems and learn from them.