You should be able to use the scan and Scan Multi buttons to differentiate between one document and one document per page. The setting that we are controlling exists in The Scan Snap Manager (SSM) or ScanSnap Home (SSH) - we just basically send that little app some commands to switch the "Profile" Paperless should have automatically set up two profiles in ScanSnap Manager or Home - "Scan to Paperless" and "Scan to Paperless Multi" - the profile switched on the fly and there are a few things that could prevent it.
1. QuickMenu - if that is enabled in the SSM/SSH then Paperless can't do it's thing - it just eats the messages we sent.
2. Wifi - if your scanner isn't hooked up via USB then the scanner seems to not like receiving those messages from the mac via USB - it's like Fujitsu didn't know we were going to make the SSM/SSH our zombie.
3. initiating the scan from the Scanner button - in this case what ever profile is already selected in the SSM/SSH will be used - this can be a great workaround by setting the profile to multi then hitting the button or doing it from the SSM/SSH.
4. some software isn't installed - we install a ScriptingAddition in the main Library for the computer - this also called an osax and it is what controls the SSM. /Library/ScriptingAdditions/Paperless Addition.osax is where it's located and what it's called.
Also to note, is that Paperless has a split document command so you can split the PDF up every n pages. That is how you can fix docs with multiple pages that you might have already scanned.
Please let us know if you need further assistance.