Accepting ACH Payments with API

I'm reading that there is a difference in processing fees if I accept ACH via invoices verses API... can someone explain this to me?  We are almost entirely an invoicing based company (no processing done in person) as a service based industry. Is there a way to get paid with API as the only ACH payment option if I am not accepting a payment in person and am sending invoices to collect payment?  (Realistically, with the new jump in subscription cost coming up -- my cost will go from $20/mo to $98/mo bc I have two "locations" in order to separate our books from the design division vs the home staging division, so I am very strong considering if it is feasible to switch back to a free plan) or if I need to find a different payment processor.

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