The way we do it is as follows:
For every sponsor we use we send a few thousand hits through our out going script. We compare our numbers to the sponsor's numbers and get a ratio. Then we put this ratio into our Excel sheet and everytime we import our data the real conversion ratios and $$$ per click are calculated automatically.
After a few months we repeat the tests. Sometimes the results are really amazing. One particular sponsor changed the counting from 1st page raw (per site) to 1st page unique (per site) to 2nd page unique (per site) and in the end to 2nd page unique (system wide for all their sites)... and all that within one year.
Well, there are more than enough webmasters that only look at ratios, so I guess it works