If you are not using Total Registration to collect payments and you want students to pay online at your school's web store, you can add a payment link to direct students/parents to make payment after they complete their registration. Go to AP => Configure AP Registration => Additional Documents and check Yes to "Do you have text that you would like to include as an additional page on the confirmation page?" You can then add a title and text and click the Link icon to add a URL link.
Students/parents will see this text and payment link once they reach the confirmation page at the end of their registration.