A chemical company often has more than one reaction pathway to make the same product. To choose between them it compares data about each one.
A high atom economy means less waste, so there is less to dispose of and raw materials are used well. A high percentage yield means more product from the same amount of reactants. A fast rate means the product is made in a shorter time, which usually lowers the cost of production. For a reversible reaction, the equilibrium position matters: if it lies far to the right, the yield of product is high.
The by-products also matter. A useful by-product can be sold, which helps to pay for the process, so a low atom economy is less of a problem. If the by-product is waste, it has to be disposed of, which costs money and may harm the environment.
For example, route A has an atom economy of 90% and a yield of 80%. Route B has an atom economy of 40% and a yield of 85%. The yields are similar, but route A has a higher atom economy and makes much less waste, so it is usually the better choice.