Sounds like your IT team messed up the setup. In their defense, Microsoft doesn't make it easy to set it up well.
A "good" setup hides all this shit from the end user. All your "library" folders (Documents, Desktop, Pictures, etc) can be invisibly made into OneDrive folders. Still save your shit where you normally do, navigate in the file manager like you normally do, no lag for changes you do locally to show locally, minor lag (like 1-2 minutes) for changes to propagate to OneDrive itself (and other machines you are currently logged into). Just now everything is backed up to the cloud.