take a site backup from your existing confluence install
install the backup on a fresh installation of confluence of the same version as your live system
copy over the now obsolete /config folder from the confluence-home directory (2.x uses this folder to store theme configs, but since it has been deprecated it will not be included in the confluence backup)
start confluence and check that everything is working correctly
uninstall builder 2.x
upgrade confluence to the target version
install builder 3.x
go to the Backup Tab and use the 'Import 2.0 space configurations' tool to import your old 2.x data (ensure that the 'associate' checkbox has been selected)
check that the data has been imported
At this point you can shut down confluence and remove the config folder since it is no longer used, you can also leave it there if you wish to be able to reimport your old 2.x data at some point in the future.