The only thing you need to run incipitor as admin for is to adjust the context menu settings. That's Windows 10 being overprotective.
There are two start menu folders - one for your own user account and another for "all users". Incipitor figures on the user's own. Incipitor doesn't merge them together like Windows does.
I, myself love to use Incipitor - I set it to my own user's start menu folder.
Also, there is "Programs" - Incipitor ignores this folder because the system uses it. I think I even programmed Incipitor not to let you accidentally rename it, too. That "Programs" folder is where all the other software will install it's shortcuts; we don't want to mess with that one.
Best thing to do is use your own user start menu folder and create some folders there and let Incipitor add stuff to those. You'll be working with the c:\users\*me*\appdata\roaming\microsoft\windows\start menu folder. That should be the default in Incipitor's settings.
Be sure and read Incipitor's help file - it explains all this stuff.