When you believe in a church's mission and trust their leadership, you fund the church's general fund. You trust the church leaders will handle the money appropriately. Very few people think they know better and fund the janitor or just part of an associates pastor's salary or pick what benefits they need. There is a trusted church administrator with oversight and input from many that determines the budget. Theyhave the knowledge to ensure all areas of the church are properly funded.
Many will initially think we will cut out the 'middle man' and fund charities directly, however the value of leadership looking at the big picture is highly valuable. With so many things needed to be funded and new ways experimented by so many charities, a board that has full time jobs of looking over all the ratings, new systems, talking to investigators and assessment organizations and other methods of exploring the best methods will make better educated decisions.