By default the ScanSnap scanners create one large PDF of every pile of paper that you run through it. But there is a carefully hidden option that lets you split paper piles automatically at, say, every other page. In ScanSnap Manager open the Settings window. Choose the File Option tab and click the Option button. Here, select ‘Generate one PDF file per n page(s)’. Enter a number into the field for n.
If you set the number of pages to, say, 2, then the ScanSnap will create a new PDF for you for every two scanned pages (e.g. front side and back side of a two-page document). — Just be sure to reverse the settings after you are finished because you’ll get (perhaps) undesirable results from your next scan of the manuscript of War and Peace.
Thank you to our forum user ‘korm’ for this great tip!