I guess my question is similar. I watched the training on Lynda.com regarding how to do SEO on WordPress. In doing so, I placed keywords in the header.php file as instructed. Those keywords are in place for every page.
Then I did SEO analysis on my site via GoDaddy tool and it complained that all of my pages have the same keywords. I guess this can be a red flag to search engines.
Wanting to have greater control, I installed SEO by Yoast on my site and am in the process of updating each page according to their recommendations.
It looks as though the WordPress meta tags trump the SEO By Yoast tags because I don't see any of the tags showing up. I see the SEO by Yoast tags in the page source, but not the focus keywords.
And while I did read that the focus keywords don't matter, I don't want to be dinged for having redundant keywords.
Here is an example page in which I applied the changes via SEO By Yoast: http://giftcardgirlfriend.com/2012/05/free-chipotle-burrito-gift-card-for-grad/