Complex sentence: The Indianapolis 500 was sanctioned by USAC, but points were paid towards the CART championship, similar to the sanctioning of three of the four PGA major championships by separate organizations, but counting as the three other most important events on the PGA calendar.
Split into simpler sentences: The Indianapolis 500 was sanctioned individually by USAC, but points were paid towards the CART season championship. It was conducted similarly to the sanctioning of three of the four PGA majors by separate organizations, but still counting as the most important events on the PGA calendar.