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I don't use GA much nowbut is it definitely not counting pages from within the site as direct referrer? I know awstats has that issue depending on how you set it up.
Sure it's possible for 1,000 people to directly type in the site. That's one of the dirty little secrets of the business. If your promo materials have your url or even a logo on them a certain percentage of viewers are going to type it in directly and the affiliate won't get anything for it. It will be tough to track these people unless you are serving all the ads and promo material. Then you could in theory track the IP address served (or use a cookie based solution) and then later see the original source if they directly type in the url. Not many companies really bother to take things this far.
For your email marketing you could place tracking links (or images) on the mailers and gather information in that way and compare it or integrate it with your other statistics. I'm not sure about GA being able to do much with that. I don't know. Only that it's possible to track it in general.
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