What are the various auto launch paths mean in OSX?

I’m trying to track down sneaky apps that launch upon reboot. They are not in System Preferences > Users and Groups > Login items and the in-app preferences for auto starting is disabled too for them. I did find them here:

~/Library/LaunchAgents /Library/LaunchAgents /Library/LaunchDaemons /System/Library/LaunchAgents /System/Library/LaunchDaemons 

What do each folder mean? Does removing the file from here simply mean the OS is won’t find it on startup?