Sage 100 should have all the NACHA specifications needed to setup your bank so you do not need to make any manual changes in the .ach file.  To learn more, see article How to Set up Payroll Direct Deposit Interface file

If you have the file layout requirement specifications from your bank, you may call Sage 100 customer support at 800-854-3415 for assistance.

I have worked with Chase Bank for decades with many different companies and got all of them to work with Sage's PR NACAH files.  Sometimes the person you are dealing with is not the correct person to be speaking with.  You're probably talking to a customer service rep and not a technician.  When I ask to communicate with a technician, I will get information from that person of what needs to be changed and 90% of the time it works.  The other 10% is going round and round, about 3-4 times, showing what they asked for IS what the raw data file is laid out correctly.  Then they come back to the 1st layout and say "your good."  

Read there NACHA document and fill out accordingly and I recommend highlighting the areas, so when you communicate with them (nowadays its email, some still talk to you on the phone) you can confirm the mandatory fields are setup correctly and others are as well.