Here is some security advice that is not only related to MAD but to servers and software hosting in general.
Don’t run MAD inside a webhosted directory like /var/www/html.
MAD does not need root privileges to run. Start it as a normal user. The only programs that need root are your webserver and your database.
Don’t use the same or similar passwords. A password manager can be useful for that.
Use SSL whenever it’s possible. Why? Read this.
It’s always a good idea to open as few ports as possible. In MADs case that’s only 22 for SSH (even that is not 100% necessary in some cases), 80 and 443 for a Webserver if you are proxying everything. Read more about iptables here.