Ryder here, from the Social Care Team at Shopify. Welcome to the Community, and thanks for posting! I'd love to gain further clarification on what route you're taking to accept payment from your customers on a later date, and see how I might be able to help!
Are you using this Afterpay Install (Unofficial) app? It doesn't look like the app developers deal with the charges at all; however, I was able to find this 'How it works' video on the Afterpay website that you might find helpful. Any further questions about the Afterpay service will best be directed towards their support team. It looks like you can submit a request on their website here. If you're just looking for any third-party "pay later" app, you can browse through a few different options in our App Store. Any questions about third-party apps are best supported by the app developers on their app page.
If you're located in Austria, Germany, or Sweden, then you might be eligible for Klarna payments which offers multiple payment options with Shopify Payments. If you're located in the United States, you can join the waitlist for Shop Pay installments here.
I hope this helps, and please let me know if there's anything I can clarify. Which "pay later" route are you taking?