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I can help answer your question about automatic ACH payments in QuickBooks Desktop.
Recurring payments are only possible for credit card payments when using the Desktop version.
Currently, the only option for ACH payment is the manual process through an invoice or sales receipt.
I don't know of any apps that integrate with desktop that would allow that ability. You can check 3rd party app options in QuickBooks by clicking on Company from the main menu: My Company: App Center.
For more insights, here's an article to check out:
Let me know if this helps.