First check which version is the version you want to keep, and which one is the one that you want to remove.
$ which dolphin-emu
and
# which dolphin-emu
should keep you different outputs. If you get the same paths, it's likely that there is in fact only one version, but since Dolphin stores its settings in your user directory (~/.config/dolphin-emu or ~/.dolphin-emu for old installs), Dolphin is not loading the same config when the user it's running as is different.
If that's the case, I would suggest resetting your Dolphin configuration by removing ~/.config/dolphin-emu completely (make sure to back up saves, your Wii NAND, etc.)
$ which dolphin-emu
and
# which dolphin-emu
should keep you different outputs. If you get the same paths, it's likely that there is in fact only one version, but since Dolphin stores its settings in your user directory (~/.config/dolphin-emu or ~/.dolphin-emu for old installs), Dolphin is not loading the same config when the user it's running as is different.
If that's the case, I would suggest resetting your Dolphin configuration by removing ~/.config/dolphin-emu completely (make sure to back up saves, your Wii NAND, etc.)