Does Squirrly SEO work with Thrive Themes?

Yes, it does. You can also use Squirrly SEO in compatibility mode. (more information about this available here)

Once you do this, the SaaS part of Squirrly SEO will help you with your SEO, and the code-changing features will be left to your themes and plugins. Also, we recently did a test for Thrive Architect and Squirrly works well with it.