Compatibility with Custom Checkout Templates

Hi. I’m using the free version of the plugin and the actual functionality of selecting deposits, paying deposits, etc. displays fine on checkout and emails. However, I use a custom template for the checkout page. The issue comes when I test using the option to pay the remainder (future payment), either from the ‘Pay’ button in the Orders page or through the email link. All I get is a default payment section with default Woocommerce template styling, which really breaks the flow of the payment and makes it seem like a separate site. Isn’t there a way to pay the remaining amount on the normal checkout page, even if it has a custom template? Or is this different in the Pro version of the plugin? Thanks.