Auto-archiving your PDFs is useful when you do not intend to re-use uploaded PDFs.
When auto-archive is ticked the PDF will be moved into the archive the next time it is sent out to be signed.
When the auto-archive checkbox is not ticked your document will continue be listed in the 'Docs' section of the site.
This 'Auto-archive when sent' tickbox appears on the PDF edit page, just above each page.
To set a default of this setting for your team, an admin user should hold down SHIFT while ticking this setting on or off.
This animation shows you where you can find the auto-archive tickbox:
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