Great question, and good to hear you are thinking about SEO as it is so key!
The way your products and collections are organized likely makes no difference to Google as it is crawling your sites content. The game changer as far as SEO is concerned is original written content and lots of it using your keywords. I have always found this video series to be the best at explaining how it all works: https://www.shopify.com/videos/ecommerce-seo-101
If you'd like more tips on how to improve SEO reach out anytime to Shopify's support team. :) https://docs.shopify.com/support
Hope this helps,