Is this Adagio OrderEntry you are referring to?

In OE, if you leave the Company Profile for auto numbering ON, then on the Posting screen for invoices, the invoice number field will be filled in with 'AUTO'. However, if you wish to over-ride the automatically generated invoice number and put in your own number, then simply change 'AUTO' to what you require. It should work the same as what Accpac Plus OE does.

If this doesn't work for you, what specific function were you wanting to do? And also why Adagio isn't performing as you hoped for?