Excise tax for late deposits - payment procedures

In the past when assisting a client with a late deposit correction we would prepare a paper Form 5330 for the client to sign and mail to the IRS with a check for their excise tax payment.

Now I understand that for most employers the 5330 will need to be filed electronically.  We have received the proper credentials to use the IRS's IRIS filing site (and have already filed 2023 1099Rs.)

Question is, how do we coordinate the client's payment of the excise tax with the e-filing of the 5330?  Can anyone share any insight on that process?

Thank you very much.

Well I see now that the 5330 is not filed using the IRIS system.  Would anyone care to share how they are now dealing with 5330s?

Thank you.

There was another thread about this. Right now there is only one approved e-filer. So I think the hope is the efiling requirement is delayed, or figured out before 7/31/2024. https://www.irs.gov/charities-non-profits/tax-year-2022-other-tax-exempt-entities-modernized-e-file-mef-providers-form-5330