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You seem to be set rather well --
From what I understand you have a main site SEO'd and then capture your audience through an email marketing program spawn of the main site which inturn directs traffic to your sales letter site where the pop is held.... There wouldn't be a problem with that... If that's what your doing it should work well - just SEO the main site - then with the emails you generate - you won't have to worry about seo on the other site.
I am not saying that all Pop ups or pop unders are bad either.... Some pop ups are actually a value to a site because they spawn a new window with more details and/or information... I'm just not sure if "G" can tell the value of the pop up....
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