It really depends on affiliate tracking scripts your merchant uses, but you have to start with unique url's for each of the keywords/pages you send him traffic from. This way you can track click-to-sale ratio for each keyword, if your merchant supports custom tracking URL's like most networks and tracking scripts..
What you should be concerned about is your keywords that make you most profit - with direct linking to the merchant you are giving them away and there's no way around it except pointing your ads to your site and JS/server-side redirecting to merchant, somehow encoding tracking parameters (i.e. keywords) so that only you know what they mean when you look at your stats.
For example, if you advertise in Google by "red widgets", your Google Adwords Target URL is yourdomain.com/?kw=red+widgets but you redirect it to the merchant, transforming your tracking keyword to something meaningless for the merchant (Of course you have to create a special database or a simple Excel table which would contain both your kws and whatever you send to the merchant. Then you will be able to track your ROI on a keyword level without merchant knowing which keyword brings you most conversions, otherwise he can easily rip you off in a bid war.. It happens all the time.
Not sure if that's the answer you're looking for, but you didn't specify the network and so on..
If PHPads you're referring to is the program that does what I tried to describe, than definately go with it.