Hello fleinbach,

You should be able to set up ACH as the payment method for one-time or recurring sales receipts. Let's get this set up first from your Merchant Services account first. 

1. Log in to https://quickbooks.intuit.com/payments/?referrer=qboblog12470. 
2. Select the Check or ACH payment method as you create a payment. 
3. Enter your customer’s bank info.
4. Get authorization from your customer. You can read them a script or have them fill out a form. 
5. Process the transfer and get paid!

In your QuickBooks Desktop, create a sales receipt, choose the payment method as e-CHECK, and check the Process payment box. This will be saved in your Manage Recurring Payments window. 

Let us know if you have any questions. Thanks!