Hi Jim,
This depends on the way IE was mapped in your old projects. If it was mapped by the ProcessName property, the old mapping should work even if you disable legacy mode since the Browser object has the ProcessName property, and its value will be 'iexplore' if you use IE. Child objects of the process/browser should also work as usual.
Regarding the legacy mode, it is project-specific. You can leave it enabled for compatibility in old projects and create new tests in new projects without it, so it is needed only to maintain your old tests.
As for switching the legacy mode on and off dynamically during a test, there's no way to do this. You can keep legacy and non-legacy tests in different projects with the mentioned option enabled and disabled respectively.
Staff