To go to the Builder>>SEO, please click Export/Import option located on the right bar of the Muffin Builder and then go to Builder->SEO tab. Now, all you have to do is click Generate button located in the right bottom and all of your Muffin Builder content will be copied straight into the Wordpress editor. This way the SEO plugin will read the content.
It is also crucial to enable the "Hide the content" option. This will hide the copied content inside the Wordpress editor and not show duplicate content on your page's front-end.
If you are using any SEO plugins, please remember to disable the built-in SEO fields inside the Theme Options.