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I would definitely add it to both as Google sees these as two different sites.

I'd also check your queries in Google Webmaster tools. You can drill down on them to see impressions by day. If you see that your impressions go to zero for a particular Keyword or keyword stem, it's a sign that you might have gotten a penalty of some kind. Penguin tends to attack pages. If you see a particular page or pages had significant falloff, it's a bad sign.

I agree with Matt, in order to get the advice particular for your situation you need a real pro that look in to your website and backlink profile but here is a general advice. If there is no manual action on your website, it’s a good part in my opinion and you have time to fix things up before Google actually put the manual penalty on it. My advice is to look in to your link profile and see how many bad links you have and separate bad links from the good one and ideally you should disavow all bad links to tell Google that these links have nothing to do with you and you are not looking for a link juice from all the bad websites. The next step is to see what good links you have and get as many relevant and authority links as you can and you will see that the rankings will go up with increase in DA as well. Again, this is a general advice for anything in particular you need to share your URL here! Hope this helps!