We created a Migration Tool for this very situation.
The manual method can be easy or complicated depending on how you are using Protect. If you are only concerned about the Patch Groups, Machine Groups, Templates etc, then all you really need is the database. Install the new OS and patch it. You will be offered SQL Express when you install Protect 9.1 on the new server. You will need to install SQL on the server before Protect 9.1 if you choose not to use SQL Express. If installing SQL yourself, I would suggest restoring a backup of your current SQL database and restore it to the new install of SQL. This will allow you to choose the database during the install process.
Please let me know if you have any questions.