There are two options how the URL of replicated site should look like. You can choose default or custom location.
This option requires a web server that supports mod_rewrite and mod_proxy modules and it will require you to add the provided .htaccess code to the location you've selected (read further).
Once you've selected the desired custom location URL and saved the banner you will be presented with 2 new buttons:
Click the Generate .htaccess for this location button and you will be presented with the code which you must add to the .htaccess file in the path defined in the custom location box, so in this example to http://www.example.com/sites/.htaccess
After it is uploaded and the correct location, you should verify if it is working by clicking the Check if it is working button.
even with site replication your affiliates can use SubID tracking, they will just need to add the &data1 or &data2 or &chan parameters to their site replication URL.
So to use the same example http://www.example.com/sites/testaff/?data1=someValue&data2=anotherValue&chan=channelCode