You won’t generally need to create a manual payment when a customer pays an invoice with a credit card or through PayPal. ZipBooks will automatically create that transaction in your account for you.
When you set up ZipBooks to receive credit card payments via Square or another payment processor, these transactions will automatically sync with your account. Paid customer invoices will sync with your books as well. You’ll also want to separate and record payment processor fees. For example, Square charges 2.9% + $0.30 for invoice payments.
Here’s how to accept payments in ZipBooks.