When a company is sourced from QuickBooks. All of the reports that we receive are formatted with respect to the company settings (Cash or Accrual) in Quickbooks.
You can change the method from Cash to Accrual, or from Accrual to Cash, by going to the company settings in QuickBooks and heading to the 'Accounting Method' property. After making the change in QuickBooks, you can update the company in Fathom (in Step 1) to reflect your results in the new chosen method.
At this stage, we're not able to provide cash-basis reporting when the company is sourced from Xero. Xero has only recently provided the ability for third party add-ons like Fathom to retrieve the cash-basis data, and we are working to build this out on our end.