Tapita does not replace your theme. The Header and Footer of your website are still managed by your theme. What Tapita does is help you modify the body section - the content between the Header and Footer. You can use Tapita to create new pages, or replace existing pages on your site.

When Tapita is installed, it creates a bunch of template files that will be used to generate your pages content. It also creates a backup of your Home page in case you replace it with a Tapita page and later want to revert back the original version.

You can check it in your Shopify Admin > Online Store > Themes > Actions > Edit code.

When you create a page in Tapita, it also creates a page in your Theme > Pages. So basically it creates a blank Shopify page, with a code to inject the content that you creates in Tapita into it.