UPDATE:
This multiple menu problem is fixed in mysql workbench version 6.3.3. I installed the new version found here:
https://dev.mysql.com/downloads/workbench/
I installed the following version Ubuntu Linux 14.10 (x86, 64-bit), DEB.
NOTE: Am am running Ubuntu 15.04. However, I installed the 14.10 version and it works just fine.
:END UPDATE
If you look closely, the menu is not actually doubled. It is actually two separate menus. The first menu is specific to the MySQL Connections home page. The second menu is specific to your open database connection. For example, if you open mysql-workbench, at first you'll only see one menu. Then, if you open a database connection and display an SQL worksheet, the second menu is displayed.
I would probably classify this as a bug because of the redundancy of the two separate menus. However, if you'd like to change the menus, you certainly do so by editing the XML for them here: /usr/share/mysql-workbench/data/main_menu.xml.
One way to do this is to run:
sudo nano /usr/share/mysql-workbench/data/main_menu.xml
You have installed MySQLWorkbench as a Snap package. You want to store the database password(s) in the Gnome Passwords & Keys facility.
However, a Snap package is sandboxed; it is not by default allowed to access this service. When you choose "Store in keychain" MySQLWorkbench is blocked by AppArmor.
You need to enter a command to allow this package to access the service. The command is:
sudo snap connect mysql-workbench-community:password-manager-service :password-manager-service
I got this from the discussion at this site.
Best Answer
Ok, This means that you need to install MySQL first, or connect to a machine with MySQL installed. Check this URL on how to do so on Ubuntu https://www.linode.com/docs/databases/mysql/install-mysql-on-ubuntu-14-04