MorpheuZ is just giving you an option to install 3.1.4 on top of your OS3.9. The option is there, because previous AmiKit X installer did not support AmigaOS 3.1.4 as a source of OS files during AmiKit installation (so I added such option to MorpheuZ at least, you know). But newer AmiKit XE installer fully supports AmigaOS 3.1.4.
Anyway, if you already installed BoingBag1 & 2 to your AmigaOS3.9 installation, MorpheuZ can install additional patches on top. Just to be sure, backup your AmiKit first. It is enough to backup AmiKit/AmiKit.hdf file and if anything goes wrong, simply use your backup file and you're back in track.
Hope it helps.