The ACH option to pay an invoice is only for customers who are signed up and approved in Pencil with their ACH details.
If you don't have any customers who are signed up with Pencil, then this would be why you don't see the ACH option for paying an invoice.
If you are referring to when a customer signs up and they don't have the option to select ACH, then this can be updated by following the steps below:
Pencil -> Settings -> Credit Forms -> Payment Terms Settings -> then enable ACH for the payment term that it is missing and Save.
If you are still the above scenarios do not apply, contact Support and provide an example or a customer so they can further assist you.