Most product-related apps require placement within the theme's product template file in order to function. In this case, using the Existing Layout product page option will allow you to use third party apps alongside Shogun content.
While the Custom Layout product page option does not utilize the theme's product template file, some apps can still be embedded.
Using Third-Party Applications With The Existing Layout
When using the theme's existing product template with your product page, your applications should work as expected and you will not need to make any additional adjustments. The applications should appear on your Shogun pages as do with with other product pages in your store.
You can learn more about the Existing layout here:
Using Third-Party Applications With A Custom Layout
If the application has an embed code available that is in all HTML, it can be embedded into Custom Layout product pages using the HTML element.
Note: Oftentimes, app developers will provide Liquid embed code for their applications (indicated by curly brackets). That code requires placement within the theme files to function, so the Existing Layout option would need to be used for the product page.
We recommend contacting the developer of the application that you are embedding. They may able to provide you with the code needed to embed their app into HTML.
You can learn more about how to make use of the HTML element here: