You can find the "Gem Fix Tool" in Windows Start Menu after installed "Gem for OneNote".
Gem fix tool is located in Windows Start Menu -> OneNote Gem -> Gem for OneNote.
In Gem Fix Tool, click "Tools" tab, and check "Run OneNote.exe at Windows start.".
Click "OK". Gem will setup auto run OneNote at Window start.
Uncheck "Run OneNote.exe at Windows start." when you want to disable auto run OneNote.