How to identify functional relations in an applied setting and is it valuable?

In applied settings there are often a multitude of variables both independent and dependent being manipulated to provide the best possible outcomes for groups or individuals. We may implement a differential reinforcement procedure for a specific behavior, while we also providing guidance on how to attend, and provide instructions properly. We may be inclined to say the differential reinforcement procedure caused a change in the dependent variable(s). But how can we be sure, and does it really matter? Are there specific rules for identifying functional relations in applied settings? If not, is it possible to create ethical, efficient, and somewhat simple analyses of the relationship between two or more variables we may use in the daily implementation of behavior analysis?