If you need a custom deployer you can configure it in the manifest file. You need to create a Java class which implements com.dotmarketing.plugin.PluginDeployer. See Creating a Plugin for more information on the configuration and wiring of this.
When dotCMS first deploys your plugin it will call the deploy method. This only happens once and only the first time the plugin is deployed. If you need to fire additional logic you must alter the manifest file with the version which will call the redeploy method passing the previous version. This is how updates are handled.