I have handled some affiliates and also developed affiliate programs for single website and as a service. I understand the use of affiliate marketing using internal application where you can track visitors and award the referrer based on actions taken by the referral.
I want to know what can you do when you don't have an internal application to track the visitors.
Yeah not clear what you want to do. You have a few options. Install a tracking script, pay on a per click basis (sketchy) or study your logs very closely :).
There are some on HotScripts, however never used any of them. Aside from the software is all the tax paperwork which is one big load an affiliate network can take off your hands.
