Usually two things to work out:
- produce the file containing the payment information as per the requirements
- transferring the file to the bank in a secure manner
Best way to get a head start is to sit down and to talk to bank you want to do ACH payments through.
Many ways to skin either cat... anything you have tried that did not work?
There should be no issues. I have FileMaker Pro to convert the check register to the necessary bank formats for ACH submission and positive payment info. For both banks, I would log into the banks' website and upload the file created. I did not need to use any plug-ins for my submissions.