Hi John-Smith! Maggie, a Shopify Partner here :)
The SEO audit, is mostly checking your:
you do it for your homepage, and then every page, even blog posts. You can use Screaming Frog free tool: https://www.screamingfrog.co.uk/seo-spider/
Ecommerce Expert at Rock Paper Copy
Doesn't get more comprehensive then this audit guide for Shopify. Shopify has a few unique quirks that I recommend understanding when doing an SEO audit.