With the release of Office 2016 Microsoft removed the ability to scan direct to OneNote. This left the only option to get scans into OneNote as being to scan to a file, and then print that file to the Send to OneNote printer. Then delete the file. Clunky to say the least.
There is an alternative.
Download iCopy from http://icopy.sourceforge.net/ and install it. Set it up to print to the Send to OneNote printer. Insert your document, click the start button and it scans to OneNote.
For a slicker setup. If your scanner has programmable buttons, iCopy can be set as a destination app. You can assign buttons using the scanner software or Scanners and Cameras in Windows control panel. Assign iCopy to a button. Insert your document into the scanner and press the button. The document is scanned direct into OneNote with one touch. Neat!