mongod stores indexes and collections in separate subdirectories under the data (i.e. storage.dbPath) directory. Specifically, mongod stores the indexes in a subdirectory named index and the collection data in a subdirectory named collection.
By using a symbolic link, you can specify a different location for the indexes. Specifically, when mongod instance is not running, move the index subdirectory to the destination and create a symbolic link named index under the data directory to the new destination.