Assuming you have followed the instructions to install a packaged version of MongoDB, you should be starting and stopping mongod using service.
To start mongod:
sudo service mongodb start
To stop mongod:
sudo service mongodb stop
If you use the service command to start and stop, it should be using the configuration file: /etc/mongodb.conf.
Starting mongod from the command line
If you run mongod directly instead of using the service definition, you will also have to specify a configuration file as a command line parameter if you want one to be used:
mongod --config /etc/mongodb.conf