My website and blog are installed on a Linode VPS configured as follows:
I just installed Yoast WordPress SEO on http://www.mysite.com/blog and was about to also install it on http://www.mysite.com when I wondered if I should be installing the plugin on just one site or the other and if there are any issues I should be aware of when installing the plugin on two sites sharing the same domain where one site is a second installation of WordPress in a subdirectory of the parent site? I am wondering what will happen if I install the plugin on both installations of wordpress and then configure them slightly differently -- will this confuse google and/or lead to penalties? Should I install the plugin on both installations of wordpress and use the same basic plugin settings on both copies of the Yoast plugin, keeping the keyword optimizations as similar as possible across both instances of the plugin?
Any thoughts/comments/suggestions would be very much appreciated.