Just install WordPress SEO by Yoast.
That’s it. Genesis Framework has built in a check for WordPress SEO by Yoast plugin (amongst a number of others SEO plugins) and once identified Genesis SEO and it’s settings is deactivated essentially replacing the Genesis SEO tools with the new plugin.
Yoast has a Genesis Theme Review in which they confirm:
As soon as you enable my WordPress SEO plugin, Genesis hides all of its SEO settings and lets WordPress SEO run the SEO show.
* Note: replacing the Genesis SEO tools with WordPress SEO by Yoast isn’t a judgement on the quality and effectiveness of Genesis SEO. It’s mostly an issue of portability for me. There is a syncing ability, but for me, and for a new installation, I prefer just sticking with the plugin I’m more familiar with.
To replace Genesis SEO with Yoast SEO Plugin simply install and activate the Yoast SEO Plugin. This will be detected and Genesis SEO will be deactivated.