Wondering if there is some sort of "best practice" for accepting ACH payments against Customer Invoices? Client of mine has a lot of items that are the same price, which means they have a lot of invoices that are the same price. They have customers that buy frequently and will send a (let's say for examples sake) $1000 ACH payment. But the customer may have 6 open invoices that could all be $1000. My client has said they just get a part of the companies name on the ACH information. Should they tell Customers upfront that the Customer needs to provide a list of Invoices they want to pay, and maybe when the payment will be scheduled for? Or is there a better way to handle this?

It will cost some amount of money (subscription fee + 25 cents per ACH payment), but they can use Stripe Netsuite connector or something like that and it will allow the user to pay via ACH with a link on the invoice, and the connector will automatically apply a payment to the correct invoice, and then deposit each payment with the daily Stripe payout. There are probably other payment processors with similar setups

adding to this point, there are solutions out there that also put a link via the customer statement so that multiple invoics can be paid via CC or ACH

NetSuite automatically applies payments to the oldest outstanding invoice for the customer. That works for some people. You could try including instructions for including the invoice number in a remittance advice section of the invoice template, but there's no way to guarantee anyone will follow it.