I don't really understand what the issue is.
The tracking code should be somewhere between <body> and </body>. If you're using the "piwikTracker" code place it before </body>, if you are using the "_paq" code place it just after <body>.
The tracking code should be somewhere between <body> and </body>. If you're using the "piwikTracker" code place it before </body>, if you are using the "_paq" code place it just after <body>.