Well because it is a script you would want to put it in the head tags.
The head tags are found in xcart/skin1/customer/home.tpl.
Any page that the customer will load will include the home.tpl (i think anyway, maybe not all pages) so just insert the script in the head tags on home.tpl and you should be right.
Also, if your having trouble figuring out what parts of the page are stored in what templates, go into your administration and on the side there is "webmaster mode" or something similar. Start that and it will show you what templates contain what on the given page.
A page can be made of up to 20 templates. All the same page.
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