will my photos, projects, and folders etc. transfer over automatically ?
Nearly automatically.
This will be a major upgrade, and Aperture will have to upgrade your library.
As a precaution, make sure you have a working backup of your library, and I'd keep a copy of the Aperture 2.1.4 Application installer as well.
Also it is recommended to repair the permissions and to rebuild the library, to make sure that the library has no corruptions before you upgrade.
Rename the Aperture Library to a name different from the default name before you upgrade.
Launch the new Aperture version by double clicking your Aperture library. Aperture will prompt you, that it is necessary to upgrade the library; let it run, this may take a while. And yes, you should find all your photos, projects, folders, etc. after the upgrade just as you imported and organized them.
Regards
Léonie