Ok thanks I had seen that topic before but I was a little unsure as to where all the files without paths were but I believe I have found them now with some help from my second ispconfig server.
About the mysql dump, will this command:
mysqldump -h localhost -u [MySQL user, e.g. root] -p[database password] -c --add-drop-table --add-locks --all --quick --lock-tables [name of the database] > sqldump.sql
backup everything for ispconfig or do I need to run it for every database on the server? I would like to know because it says "[name of the database]".