There are two kids of custody: physical custody and legal custody. Legal custody has to do with decision making regarding the children, and parents commonly share joint legal custody. Generally, with joint legal custody, day to day decisions are made by the parent with whom the children are at the time the decision is to be made. For example, if a mother has primary physical custody, but the children are with their father for the weekend, then the father is entitled to make the day to day decisions that are needed or desired during that weekend.
Decisions concerning education, health, religion and extracurricular activities are frequently treated differently. These decisions are generally considered "major decisions" which are to be discussed and agreed to by both parents. If the parents cannot agree, one parent gets ultimate decision making authority. For example, one parent could get final decision making authority for all major decisions, or the parents could split final decision making authority with one parent getting health and religion and the other parent getting education and extracurricular activities.