Yes, paste the code into the layout.master file of your skin just before the closing body tag:
<!-- Woopra Code Start -->
var _wh = ((document.location.protocol=='https:') ? "https://sec1.woopra.com" : "http://static.woopra.com");
<!-- Woopra Code End -->
Of course there is no point in putting it there until they approve your site. You have to sign up and get on a waiting list.
ps: Tip: When pasting code examples or markup in the forums, use the "Paste as Text" toolbar item (clipboard with a T). In IE, it uses this automatically but in FF you have to click the button.