When the plugin first loads, a config.yml file will be created in the MagicSpells folder within your plugins directory (as of version 2.11, multiple yml files will be created, and the config.yml will no longer be created). The default configuration has fairly reasonable spell costs, durations, and messages for each spell. However, it is mostly just an example, so you will probably want to customize this to fit your server.
To reload the configuration, simply cast the fake reload spell (
/cast reload). Only server operators can do this (it can also be done from the server command line).
You may also want to set up the Permissions for the plugin.