Does Piwik Work With Cloaking

Please help me answer this question as i`m not sure exactly how the tracking works. I want to cloak my website, but I think that the tracking will no longer work since it wont load my actual site, it will load my “pretty” site. So, should I then put the Piwik tracking code on the “pretty” site to see how many visitors I am getting there, from where etc?

Please advise. Thank you.