Robynne, you can add the children to each parent separately or add the mother and father to each child separately.
When adding children, look for the checkbox above the ADD CHILD OF ... button that says "Uncheck this if ____ is not the other parent" to prevent the spouse of one parent from being connected as the child's other parent.
When adding parents, look for the checkbox that says "____ is the father's spouse" to prevent one parent from being connected as the other parent's spouse since they never actually married.
By unchecking these boxes, you'll avoid making extra relationships and each child will have the correct mother and father.