If the links on the first website redirect to 2nd site, and the header tells it to redirect to amazon then it wouldn't really work. But I believe using nofollow tags should prevent the search engine from following to 2nd website.
Most people just randomize how often to show affiliate links or...
Piwik is another alternative if you can't figure out how to use Google Analytics. But as IMpossible stated you might have messed up including the javascript into the page.
I've been rotating domains using a back-end script and Chrome has slowly been blocking them one by one however I find this method to better than double zipping.
Make sure the script downloads directly from the PPI company and scrambles the name of the file.
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