Hello GPManiac,
Yes, of course GP supports multiple addenda records in the NACHA formats so PPD and CCD formats would be able to do this. (However, the IAT format does not.) If you mark the 'Detail line addenda' checkbox, then one remittance line will print for each invoice that makes up the payment for the PPD/CCD formats. So if 3 invoices make up the payment, then 3 addenda lines will print below it, if 12 invoices make up the payment then 12 lines print,etc... However, remember to map the fields for the Addenda line, where KB 2956922 comes in handy to show you to pull the 'Apply to document number' from the PM Apply to History file. You can only get to the fields on the invoice that are in the 'apply' table to the payment (apply amount, date, discount), so you would not be able to pull other fields on the invoice such as the invoice description, PO#, original doc amount (if credit memo's applied), etc.
See Questions 4, 19 and 20 in KB 945955. http://support.microsoft.com/help/945955
I hope that helps.
Thanks
Cheryl Waswick
Microsoft Dynamics GP support