Correct. You need to use the PluginRegistration.exe tool: http://code.msdn.microsoft.com/crmplugin/Release/ProjectReleases.aspx?ReleaseId=2010
Then connect to your server and org. Find your plugin and double-click the plugin step. You will get a form popup and in the bottom box on the right you can enter the Secure Configuration.
In your plugin make a constructor something like this to retrieve the unsecure or secure string:
private string _key;
public EncryptorPlugin(string unsecure, string secure)
{
if (!String.IsNullOrEmpty(unsecure))
{
_key = unsecure;
}
if (!String.IsNullOrEmpty(secure))
{
_key = secure;
}
}
They are basically the same except the secure string is a little harder to find and encrypted in the database.