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I am not sure of the seo implications, but I would do everything I could to keep 1 installation if I could. It just seems like it would make management a lot easier. I may not be following what you are asking though. It sounds like you have a site without a blog using 1 worpress theme and then you are wanting to add a blog using another wordpress theme, is that right?

Thanks for the response.

Well, from an administration perspective, we have multiple sites already... so I certainly know the challenges and amount of time that can take. I personally am leaning toward having only one site, but am looking for some reasons why one strategy may be better than the other. I was wondering more from an SEO perspective since the administrative complexity would only be simplified with one site.

I also agree, any answers I get will probably be sweeping generalizations without knowing all the specifics of our business, and analytics.. so I am taking that into account.

We had a similar issue, with thousands of duplicate content pages. Most of these were pages that didn't really need to be indexed. For instance, our store has a review feature where customers receive an email a few weeks after ordering to review the product they received. Every product has a unique url for this but the pages aren't really meant to be accessed outside of the email so they were not optimized and we didn't really have a way to optimize them. We felt they didn't need to be indexed. So, we added some disallows to our robots.txt file and that cleaned most of them up, leaving just the legit duplicate content that we wanted to get fixed.

The jury is still out on any kind of seo improvement but it stands to reason that the crawler will be able to find the important pages on our site much quicker and no longer is seeing duplicate content.