You can find the command with the help option.
yunohost --help
you see that it exist the settings argument
Then, you call again the --help option:
yunohost settings --help
and now you can read:
list: list all entries of the settings
and
set: set an entry value in the settings
Now, you know all the settings you can manage 
yunohost settings list
And i find the option that you search:
sowat.panel_overlay.enabled:
default: True
description: Enable SSOwat panel overlay
type: bool
value: True
and:
yunohost settings set --help
usage: yunohost settings set key [-h] [-v VALUE]
set an entry value in the settings
positional arguments:
key Settings key
optional arguments:
-h, --help show this help message and exit
-v VALUE, --value VALUE
new value
it only remains to pass the command line:
yunohost settings set ssowat.panel_overlay.enabled -v False
You can find a lot of things with the --help option (not all are well documented
unfortunately)
That’s right only if you edit the files directly. The good practice is to use a hook to allow the updates and use some custom configurations.
the hook /etc/yunohost/hooks.d/conf_regen/17-nginx_yunopanel that you can find in the link of my previous post do the same.
When the ssowat.panel_overlay.enabled setting wasn’t avalaible, it was the right way to remove the logo.