The conf.d directory actually works a bit differently, you cna think of it as if all the config files are combined into a single config. This means if you want to connect an input plugin to an output plugin, you need to use the [metric filtering](https://github.com/influxdata/telegraf/blob/master/docs/CONFIGURATION.md#metric-filtering
). In the absense of any filtering all metrics produced are sent to all outputs.
Override behavior isn't possible, and it's not something the current TOML could support. A new plugin is created for each plugin table found in the configuration files. Recall that any `[[tables]]` with double brackets is TOML style for a list of `[table]`, so you can read double bracket as the item can be specified multiple times. This allows you to have as many instances of a plugin as you need.
It's not required, but when using the conf.d directory and a split configuration, I usually remove, or disable, everything other than the `[global_tags]` and `[agent]` table from the main telegraf.conf and place all plugins in the conf.d directory.