Hi, Bruce,
'Keep PDF accounting copy' just keeps a second copy of the output in the folder of your choice. This second copy can use a different spec than the spec used when the document is originally printed.
'Archive Customer copy' always places the copy in the a SOFTPDF folder within the data folder. Among other things, this can be useful as it is a known location regardless of the site's other settings.
For example, per the Help, the new PDF Viewer button being rolled out in modules (eg. AR9.1A customer Transactions, etc.), looks for the PDF documents to display in the SOFTPDF folder. As well, in Receivables 9.1A, the 'Attach unpaid invoices' option for Statements also looks in the SOFTPDF folder for any PDF documents to be attached to a statement.
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Regards,
Softrak Tech Support