Indicate to Google that two websites are two separate companies

I currently build two websites for two different companies. Each company runs PPC campaigns from these web sites.

If I use the same common files to build the two websites, would Google detect them as the same company? That's something I don't want. I want Google to see them as two separate companies.

Added to this, the two websites are hosted in the same server. And they share common files.

I have them share common files since they are similar in design and helps me have a cle开发者_开发知识库aner code base.

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There's no problem. Many people do this -- use the same files to create different websites that are near clones of each other. Google's not confused by this. Furthermore, Google does not even care about companies, per se, because it doesn't search companies; it searches web pages. As long as they have different URLs, that's all that matters.

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Google has no problem understanding that they are two different websites.

However be aware that Google also checks for duplicate content and has tests to detect (and penalize) things like link farms and content farms. If the two websites look similar and have almost the same content, this could become a problem. If the content differs (which it almost certainly will for legitimately different companies), then it is a non-issue.