Click tracking code should be stored into file skins/<skin_name>/customer/footer.tmpl
If you don't have this file in your skin, just copy it from skeleton directory to your theme directory and add click tracking code, which is prepared for you in Post Affiliate Pro (menu Tools -> Integration -> Click tracking)
Add this code before </body> tag in your footer.html template.
Because Summer cart integration can't use Flash cookies tracking (only browser cookies are used), we will need to disable flash cookie tracking, by adding following line to click tracking code:
It should be stored right after line
PostAffTracker.setAccountId('default1');
in your click integration code in footer.tmpl file.