It is not necessary to purchase an additional license to process transactions for more than one company.
If you are processing payroll for three companies, and each has one bank account, you would create three separate Accounts within ACH Universal. There is a one-to-one relationship between each bank account and each ACH Universal Account.
The Standard/Desktop edition of ACH Universal, by default, comes with 15 available Accounts. If you have a subscription license, as a supported customer, you may request as many Accounts as you need. If you have a traditional license, requesting additional Accounts would be considered an upgrade. (Pricing for additional Accounts may be found here: https://store.treasurysoftware.com/category_s/89.htm )
If you are a third-party processor (e.g., CPA firms and payroll processors), and you are processing ACH transmission files on behalf of many companies, you should be licensed at the Processor-level for multiple-origination transmission files.