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Nevermind the fact that this sounds totally strange... the two sites do work together in this way, and it's a lot more sensible than it sounds.
So, my tiered question:
1. Can you have one AdWords account that contains 2 analytics profiles and feeds data to them accordingly based on where the clicks went?
2. If so, can you do it within the same campaign, or do you have to create a new campaign?
3. If you can do it within one campaign, can you run ad variations within one ad group that deliver to two different sites and get accurate metrics from that? Or do you have to run ad groups exclusively for each site.
Thanks for any assistance!
2. I would *strongly* advise you to create separate campaigns for each site - and if you're advertising in content and search, you should create two campaigns for each site.
You can specify a profile for each site, and then tell it which domain to include the AdWords data for.
But I can't off the top of my head see the scenario where your #3 would be useful, so I can't answer that one.
If this is the case you want to have 1 campaign set up with 2 identical ads set to rotate, each going to a different URL, and 2 conversion goals set up for the campaign, one for each site.
Alternatively you could set it up so you have 2 accounts, so the ads for the two sites would run side by side, but you would have 2 problems with this method, in order for it to be a fair test the ad text would have to be identical, which would look odd, and you would spend more money through people clicking through to both sites when they are shopping around.