This doesn’t actually affect the Printout Manager unless you decide to split the printout pages onto separate OneNote pages. Once that happens, OneNote will recognize that some of the pages are missing and display the above message. It doesn’t prevent or break anything, it’s just more of an annoyance than anything else.
To use the OneNote Printout Manager, simply download the file at the bottom of this blog post onto your computer. It contains installation files for both 64-bit and 32-bit versions of OneNote. Install the most appropriate one for your particular installation of Office. Once you have the OneNote Printout Manager installed, click Insert –> Printout Manager and you’re set to go.