Not to brag but, one of the schools we look after at work has been granted Microsoft Showcase School status.  #winning
Part of that status is to do with how the school have adapted and run with OneNote for teaching and learning.  Teachers in the school use the Class Notebook Add-in for OneNote and so here’s my experiences with deploying it.
The first version I came across was and was a downloadable .exe file called ClassNotebookSetup.exe and to get this into ConfigMgr and deployed to clients we wrapped in with a simple batch file after we interrogated the .exe for silent commands we got this:
Excellent.  So I created an application using manual methods (having the correct Office version as a pre-requisite) and using the silent install commands above and boy did I have strange results!  So weird in fact that I lost quite a bit of time to trying to figure out what the heck was going on and took to Twitter to vent my frustration to say “Why isn’t this an MSI!!??”.  In the end I discovered that if I wrapped the application with a simple batch file it worked without error.  So in the folder where the .exe was I create 2 simple batch files with the following lines of code:

   1: ClassNotebookSetup.exe /install /quiet /norestart

   2: md c:windowstempClassNotebook

Funny because that silent install command on the first line is precisely what I used when I originally created the application but you know, whatever.  I used the ‘make directory’ line so that we could use that folder as a detection clause.  I like doing this because if for some reason you want the application to re-install you can tell the engineers onsite to delete this folder and it will pull back through.
For the uninstall we made a second batch file containing this:

   1: ClassNotebookSetup.exe /uninstall /quiet /norestart

   2: rd C:WindowsTempClassNotebook

This time uninstalling the software and removing the detection clause folder.
Now, Just recently a new version was released. Currently and can be downloaded HERE but if you click on Other download option on the bottom of the page it will take you to the download for IT Administrators which……… is a MSI!! (Thanks Mike Tholfsen!) .
You can directly download it from HERE (link subject to breaking)
Pretty straight forward task to put an MSI into ConfigMgr.  Once that’s in you can then deploy that using application supersedence to deploy the new version and uninstall the old version.
I have tested this and it all works just fine in my lab (ConfigMgr 1602 + Windows 10 and Windows 7 clients), I’m now happy to push this in production.
PROTIP! Developers don’t rename their products normally so I have gotten into a habit of ensuring the name of the app and the version number is in the name of the app within the console and the software catalogue.  For example if I use the defaults for this class OneNote, the default name is Microsoft Class Notebook Add-in for OneNote and guess what?  So is the new version. Therefore if you add the applications into ConfigMgr with the version numbers on the end and ensure the software catalogue also has the version numbers on the name before you distribute the content anywhere its easy to differentiate between them inside the console and on the clients.  Forget this step and you’ll have weird results.
I hope this is useful for you.