Piwik and Sharepoint 2010 (no replies)

I know that Piwik support Sharepoint 2010 and it is possible to add tracking code to the certain page and that solution works perfectly. What if I have a hundreds of Subsites and a hundreds of pages inside of it as well ?
Should I paste tracking code into masterpage or rather somewhere else?
What is the "Best practice" in this case ?

Thank you in advance