How can I solve my shipping confusion?

OK, I need a definitive answer about shipping rates. So Shopify tells me they won’t allow me to use their shipping because of my products. So I use Pirate Ship which I love. My question is this… can I delete all my work adding shipping details to Shopify and not mess up my shop? I’m always afraid of doing anything because this Shopify is so touchy. Can I delete all my Shopify shipping settings?