You get to decide the ranking when chopping players. On the "Edit Prize Chop" dialog, on the right side you'll see "Ranking" with two columns "Relative" and "Actual". The "Actual" column shows what rank the player will actually receive. In the "Relative" column you put in numbers (any numbers) to order the players and thus derive their rank.
By default, the Relative column will have zeros in every row. This means every player has the same relative rank, and thus will end up with the same actual rank. So let's say your last 3 players decide to chop. By default they will each rank 1st place. If you give one of the players a Relative rank of 1 (or 2 or any number greater than 0), he/she will rank 3rd, while the other two will remain at 1st. Basically, you are putting the players in an order, with "ties" allowed. The software will provide the actual rank. Try it out, putting different values into the Relative columns. The numbers themselves don't matter, just the numeric order they create.