A Microsoft Team is the persistent chat and channel functionality added to an Office 365 Group. An Office 365 Group automatically creates a SharePoint site and a OneNote notebook in the Site Assets folder of that SharePoint site. I love this Everyday Guide to Office 365 Groups by Matt Wade that illustrates this relationship very well: https://www.jumpto365.com/infographics/everyday-guide-to-office-365-groups. It is a better practice to use this associated OneNote notebook as it is automatically inheriting permissions. You can create additional OneNote notebooks in the connected SharePoint site as needed.
Since the notebook is in the cloud, team members can choose whether they want to open that notebook in the Teams desktop or web app by adding it to a tab. Team members can also open the notebook in Windows 10 app or OneNote 2016. I think it comes down to personal preference for which is best.
I prefer opening all my notebooks in OneNote 2016 as it can create custom To Do tags, which the Windows 10 app does not. As a consultant, I also find myself emailing pages to external meeting participants as they do not have access to the notebooks. Selecting "Email Page" from the OneNote 2016 app will open a new email in my Outlook desktop application. "Email Page" in the Windows 10 app will open the Windows 10 Mail app, which I do not use.
Let me know if I am understanding your question correctly or can provide more guidance :)