I'm probably missing something here but don't you have to install the beta to get the revised manual?
Yes.
And--when you do--it overwrites your preferences even if installed to a different drive/directory.
No. The installer doesn't know anything about the various preferences files. It won't touch them (either when installing or uninstalling).
The preferences files are created on-demand. When the software starts, it looks for the preferences files to read them, and if found, it does so. If not found, it uses the default set of preferences (built into the application) and creates new preferences files.
The software has been designed to be able to load preference files, tournament files, templates files, etc, from any previous version of the software. So you shouldn't ever lose your preferences when upgrading. Even if you upgraded from version 2.0 straight to version 3.2.b2. That's how it's
supposed to work (and does in my testing). But as I always note, make a backup. That way if something does go wrong, you don't have to lose your preferences.