Although I’ve had DT Pro for sometime, my wife is on me to get my office “organized” and now I want to use DT to do that, but I have tons and piles of paper to scan with my ScanSnap and need some “quick start” suggestions.
I put in the ScanSnap a pile of receipts and it scanned them just fine except they all scanned as a group like they were all related to each other and they are not. So, the question is, how to separate them and how to avoid this in the future?
To avoid in the future, put one document through ScanSnap at a time, and you’ll get individual files for each document. If each document is the same length (say, one page or two pages each) then there is a ScanSnap setting to make a new document every x-pages. (Don’t forget to undo this setting with you are finished with your tonnage. 
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For the large file you now have, display it in DEVONthink with the sidebar showing (View > PDF Display > Sidebar. In the sidebar, select the page(s) that represent a single document. Press copy (command-c) and then Data > New > With Clipboard (or command-N). This will create a new PDF with just those pages in the same group. The original PDF will remain intact.
(It is possible to drag pages out of a PDF to create new documents, but in that case the new document is a TIFF file, which is not helpful.)
You can set up profiles in Scansnap manager appropriate to the task. Eg I have created a profile which I have called “Stack of Single” which is suitable for a large number of separate single sided documents which are automatically saved as individual PDFs. The docs don’t have to be fed in individually. I have another for double sided docs which I want to be separate PDFs.
I strongly recommend “The Unofficial Scansnap Setup Guide”
…where I learned about profiles and a lot more.