Upon initial installation and using the automatic option:
Your theme may be displaying the new price button a different size, shape or position to which you desire. All product templates in Shopify are slightly different depending on the theme and so If you have no luck with the tools from within the app, you will have to set up the button manually. This will give you full control of the look and style of the new button.
If you need more help with setting up the button, you can use a service like StoreTasker.