Use your FTP utility and look for the file:
PluginOrganizerMU.class.php
It will either be in your:
/wp-content/mu-plugins/ folder (where you want it), or
/wp-content/plugins/plugin-organizer/lib/ folder (where you don’t want it)
Normally, you can use your WordPress admin interface and, at the bottom of Plugin Organizer >> Settings, move the Plugin Organizer to your /wp-content/mu-plugins/ folder (create a folder “mu-plugins” if it doesn’t exist).
For me, the move function wasn’t working properly, so I manually downloaded PluginOrganizerMU.class.php, deleted it from /wp-content/plugins/plugin-organizer/lib/ folder, and uploaded it to the /wp-content/mu-plugins/ folder.
If you don’t have that file and need it, go to https://www.ads-software.com/plugins/plugin-organizer/developers/ click the current version, then click /lib/ and right-click PluginOrganizerMU.class.php, “save link as” and upload it to your /wp-content/mu-plugins/ folder.
Lastly, I think Jeff intended to make Plugin Organizer SSL-friendly with an update about a year ago. So technically, you should be able to go into Plugin Organizer >> Settings …. Ignore URL Protocol and set that to enable.
For some reason, however, when I enable this option, all my my plugins that are globally disabled will remain globally disabled. I’m still seeing if I can figure out if it’s my fault on these domains, or something Jeff might have skipped over by accident, so I’m checking.