Very simple, they are counted only those empires in the top 500 of each game. Collect as many points as 500 minus your rating classification and the winner takes 500 points, the second would take 499 and so on until 1 point for classified at position five hundred.
In addition bonus 1000 points to 1, 900 for the 2nd, 800 to 3, 700 to 4, 600 for the 5th, 500 for the 6th, 400 for the 7th, 300 to 8, 200 for the 9th and 100 for 10th place.