No, he didn’t (@ryand, if I may). He means that you do not need both fans running at the same time. You should always* have at least one fan running, but you shouldn’t need both. So, if you’re using your external fan, set the UI to use the filter, which will turn off the internal fan. If you’re not running your external fan, then turn the internal fan back on.
There’s also nothing to prevent you from removing the existing internal fan entirely if you’re going to use your external all the time. This will improve your external fan performance, as there will no longer be the old fan obstructing your airflow.
* There are very narrow limited exceptions, where you could argue that a fan isn’t needed (engraving aluminum, some other no-fume actions), but they’re so infrequent that it’s safer to simply say that you should always have one fan running. This is especially true with pro models, where the active cooling system is reliant on the airflow.