Sensors and Broadcasting
The gist of it is to design flyers to be both sensors and broadcasters, and the Wraith to act as the command center.
The flyers themselves would probably need an array of sensory organs, such as sight, smell, and hearing, which they could transmit back to the Wraith through the same broadcasting mechanisms. This broadcasting mechanism could act in one of two ways: by pheromone signals and 'sound packets'.
Wraiths could use pheromones to communicate with the tiny creatures by releasing certain pheromones for different commands; similar to how we can smell fear.
As mentioned by @awsirkis, if the flyers are truly single-celled organisms, this could be done through a process called Quorum Sensing instead, but I will continue to refer to it as pheromonal transmission.
As to how it does this, the Wraith can function like a command centre. The small flying creatures, upon entering the Wraith, can bring back valuable sensory information (eg sight, smell, sounds) as they recharge nutrients, as long as they are equipped with small sensory organs.
Relying on this sensory information, the Wraith can output detailed Pheromone instructions, which is carried by the returning flying creatures.
These creatures can then transmit the pheromones to nearby flying creatures, acting as broadcasters. The Wraith would thus be able to command the flyers to do complex tasks with different commands for flyers in different regions.
This would make make the Wraiths weak in an interesting area: smell. By making use of tactical stink bombs, and overloading the capability of the flyers to sense pheromone commands, the Wraith would become disoriented and unable to properly control the flyers. As mentioned by @zovits in the comments, this would also imply a weakness to windy areas, which could possibly limit the accuracy of the pheromonal transmission.
It might also have an issue of latency; commands may get disrupted due to smell itself lingering for far longer. This would mean that the Wraith would have slightly delayed reactions to circumstances.
Broadcasting with uniquely identifiable sounds
Another alternative is a similar system, but with 'sound packets'. The best parallel to our modern world is of the Wraith being like a wifi router, sending packets to the flyers, which are like phones/devices.
How the system would work: when each flyer is born, it gets a unique ‘sound id’, like a ‘name’. The 'sound packets' would consist of a front portion with the 'sound id', and the command itself. By receiving information like sensory info from sounds made by the flyers, and transmitting commands to the flyers as 'sound packets', the Wraith can command the legion of flyers either one by one, or as a region by grouping certain ‘names’ together.
The 'sound packets' will be heard and re-broadcasted by the flyers as needed, and the flyers can figure out if the 'sound packet' is for them by recognizing the 'sound id'. The sound waves themselves would probably be quite high-frequency, as this would allow for more waves in each sound packet, and being able to send out more commands in less time. It would also allow for an advantage of nearly-instant commands, as compared to pheromones.
This alternative also carries the weakness of being disrupted by sounds of similar frequencies, but a weakness can make the Wraith more interesting. The Wraith would have to spend extra effort to smother sound sources or knock away flashbangs, which could completely disorient their command structure.
Something interesting about using sounds to command a cluster of flyers means that the Wraith could potentially use the sound as a weapon; by inducing enough flyers to transmit sounds continuously, the target's inner organs can be damaged through the vibrations, or the target can be severely disoriented by thousands of ultrasonic signals sent through the flyers.
Once the target has been subdued, the Wraith can come close enough to the target to drain them of their essences, fitting with the image of the Wraith. (Due to the high-pitched sounds, you could even give the particularly powerful Wraiths the nickname of 'Banshee', as hearing their screams means the omen of death).
Both these ideas would make the Wraith like a murderous flying hive accompanied by either a unique orchestra of smells or a cacophony of buzzing.
Misc: the idea of unique 'sound ids' comes from the real-world communication protocol called Universal Datagram Protocol (UDP). This is used for connection over the internet, between devices. Essentially, packets consisting of an id and data contents are sent from one source to all connected devices, and they check the 'id' to see if it is for them before unwrapping it and using the contents.