I always used to use the audit program in the NACHA ACH Operating Rules & Guidelines book, which just listed the procedures that were required and didn't give much guidance in completing them.
It's been at least a few years since I've done an ACH audit myself. I checked out the Audit book referenced by SarahH. If I would have known about this resource, the cost seems like it definitely would have been worth the extra time I always had to spend trying to interpret it all myself.
From the nacha website:
The updated ACH Audit Guide 2005 is offered for the first time this year as a spiral bound workbook with an included CD version of the guide. The CD version will allow users to enter their audit information electronically. This is a comprehensive, working ACH audit document with tools to enable you to more easily perform the annual ACH audit required by NACHA. ACH Audit 2005 is designed to specifically outline each exposure point financial institutions and third-party processors are required to test. The workbook can be completed by internal or external auditors, or ACH management. The guide includes instructions on how to complete the 2005 Audit, specific rules corresponding to each ACH requirement, and testing instructions for each specific exposure point. Each area of ACH is included for review: originating, receiving, exception item processing and Treasury issues. Examples are provided for easy understanding in the introduction of each section. The Guide also includes ACH terms and definitions for quick reference.