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 to be listed in the Document Library 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 video shows you where you can find the auto-archive tick-box:
Docs can be pinned to the dashboard (in the left hand column). If you pin your document it will continue to be listed there even if it has been archived.