Do customer payments sync to QuickBooks as well?

Yes, once you pick a bank account for payments in the QuickBooks account mapping. Each new payment recorded in BytePhase is posted to QuickBooks as a Payment linked to its invoice, and if that invoice has not gone across yet, BytePhase sends it first. Leave the bank account blank to skip payment sync. Only newly recorded payments go across; editing or deleting a payment after it has synced does not change it in QuickBooks.