If you use QuickBooks, apply for QuickBooks Payments through the software. Here is how to set up ACH payments in QuickBooks in a step-by-step guide. This guide includes entering more account information about your business. It will also go over your merchant account number to use for the system. ACH transfers are safer than wire transfers and paper checks. That’s because, with wire transfers and paper checks, routing numbers may be shared. Fraudsters enjoy devising wire transfer scams that include phishing and altering paper check amounts.