When using the Mark as Paid feature in AutoEntry and publishing to Xero, the setting for how the invoices are published to Xero must be set to Awaiting Payment on your company's Integrate page.
The payment will not sync through to Xero if Draft or Awaiting Approval is selected.
There are two options available for where to publish these invoices across to Xero:
If Publish To is set as Purchases, AutoEntry will create the purchase/bill and a spent money transaction against this purchase/bill.
If Publish To is set as Bank Account, AutoEntry will bypass Accounts Payable and instead immediately create a spent money transaction.