You can edit values of server.properties, bukkit.yml, spigot.yml, and paper.yml in your server dashboard under the Settings tab. You are not allowed to openly edit the files above as there are some values in the file that should not be accessible to Minehut server owners, such as the bungeecord value in the spigot.yml file, which could break some stuff with your server; the server-port value in server.properties, which you could mess with the port and in turn make other servers not start if they are running under the same port as the value you've changed; the online-mode value, which can allow cracked clients to join your Minehut server which may break some functionality of the plugins on your server.
If you have suggestions to add to the Settings panel, just suggest them!