In 100 and 500, Sage has a solution for AP. I believe they still charge a transaction fee based upon a percentage of the dollar amount of each transfer. However, most of the time, this isn't a significant cost.
I agree with Wayne, reinventing the wheel is not the best way to go. If you can use a tested solution, take it.
Also, I believe Kevin Martin at Martin and Associates wrote a custom solution in 100 for a customer in the past to process automated AR collections through ACH. I don't know that the 100 interface with SPS covers the AR side of the house like it does in 500. If you have recurring billings and can get a customer to sign up like your utility, it's an efficient way to reduce days open is AR.
In our case, the client was processing $2 to $3 million in ACH transactions per month. The average transaction was about $250,000. Paying 1 to 2% of the transaction amount as a processing fee was not ecomonically the right way to go. Thus why we went to the trouble of writing something custom.