Conversion is measured at each step of the player’s path: a click on the link, a sign up, a first deposit. The conversion rate is the number who moved to the next step divided by the number at the previous one.
Example. 1,000 clicks, 80 sign ups, 24 FTDs. Click to sign up conversion is 8%, sign up to FTD 30%, click to FTD 2.4%.
When you compare programmes, look at click to FTD conversion on the same traffic: a programme with a lower commission rate but better conversion can earn more.