Remove the MySQL daemon from startup with the Debian Runlevel configuration tool, rcconf. More details about this tool is here:

http://packages.debian.org/stable/admin/rcconf

Install the tool with APT:

sudo apt-get install rcconf

Then run the configuration tool:

sudo rcconf

This will display a basic GUI that will allow you to uncheck the MySQL daemon, mysql. There may be two other MySQL related items, mysql-ndb and mysql-ndb-mgm. It is not essential to disable these administrative services to prevent the MySQL server from running. To start the daemon manually enter:

sudo /etc/init.d/mysql start

To edit the configuration before starting the server, run:

sudo nano /etc/mysql/my.cnf

Verify that the server is running with:

mysqladmin -u root -p version