This was very helpful (as were the other two replies) so I am hoping you can help clarify how I can get this addressed. (going with list format to simplify):
1- I tried to set up my campaign to look at the root domain, but it said that my website is set up as a subdomain automatically converted this step of the process to "subdomain".
2- SEOMoz Pro did tell me at some point in the setup process about what you mentioned above, which is that there are two versions of my site. This may have been at the setup point where it converted root domain to subdomain, though I can't recall.
3- When you say "choose" one version of my site, do you mean as far as what SEOMoz crawls? Or are you suggesting I make a change to the site itself?
4- The blog is, I believe, set up as a subdomain (with www.blogs.aerohive.com) and it is hosted by a third-party. I set up the dedicated blog campaign as a subdomain, but had some difficulty with it as well. Not sure if that was correctly set up or not.
Basically I am trying to understand what was set up correctly or incorrectly within SEOMoz and what can fix and what I can fix with my website so that I can better analyze it here (and obviously get search engine approval as the ultimate goal).
Thanks,
Amanda