Bill.com sends funds via ACH in CCD format. Generally speaking, that means that fund distribution go to the payee's cash or liquid account (fro example checking accounts, savings accounts). If the funds then need to go to a brokerage account, it's the responsibility of the recipient of the original payment to move the funds to that secondary location. As I understand it, a mechanism can be set-up to automate the transfer the funds from the bank to the brokerage firm. That's something that the brokerage firm should be able to assist with.
What Bill.com can't do is send funds to an account that requires a secondary movement of funds based on an FBO notice. In these situations, the funds being distributed must first go into the bank account of the financial institution holding the payee's security/bank account before it is transferred to the intended FBO. Bill.com does not have the ability to send FBO instructions so we do not send funds through that model.
We have seen exceptions to the "no brokerage accounts" rule though. We've seen a program through Merrill Lynch where all fund distributions are sent to a unique account through Bank of America. In this case, the bank and brokerage firm worked together to create a unique account number comprised of bank account details and the brokerage account number. This allows us to send the funds directly to a brokerage account, but through an ACH process that looks exactly like a bank deposit. There may be other companies that have a program similar to Merrill Lynch. Normally, the details of how the payment will be processed for deposit is clearly explained on the direct deposit authorization form.