The project's README.txt file states that the default format for affiliate links — "/affiliate/[uid]" — can be overridden by adding to the site's settings.php file a line such as the following:
$conf['uc_affiliate2_path'] = 'my_affiliate_path';
This should change the affiliate link format to "/my_affiliate_path/[uid]".

But this does not seem to work. For instance, if the user ID for an affiliate is 1, then visiting any link containing "/my_affiliate_path/1" should give credit to that affiliate. Instead, no click credit is given to the affiliate, and the visitor receives a "Page not found" error.