The SMC04 is a very nice controller with a lot of features, but it is only set up to control DC brush-motors. It outputs a single PWM power signal, which makes the motor act as if you were controlling the voltage you applied to it (which you are, sort of). The Astro Flight 020 is a three phase brushless motor, which needs three separate power signals, with some interesting timing and duty-cycle control.
Remember for a second how a DC brush-motor works. The pins on a brushed DC motor are connected to two brushes, which make sliding contact with the stator (the cylinder with electrical contacts that rotates with the drive shaft). These contacts transfer power to the different parts of the armature, a set of thin wires wound around a core also connected to the drive shaft. As the shaft spins, the different stator contacts either reverse the direction of current flowing through the armature windings, or power different windings on the armature depending on the motor design. The current in the windings produces a magnetic field, which interacts with the field of a permanent magnet, or a set of permanent magnets spaced around the armature. These magnets are connected to the housing of the motor, so the driveshaft is forced to turn with respect to the housing. With this design, any DC voltage will cause the motor to turn, and the motor output power (torque & speed) will be proportional to the supplied voltage.
A brushless motor, as the name implies, has no brushes. In fact, there is no electrical contact between the driveshaft and the base. In any brushless design, the permanent magnet or magnets are connected to the drive shaft, and a set of coils are stationary, connected to the base. Which is on the inside and which is on the outside depends on the motor. I’m referring to the base, not the housing, because sometimes on small brushless motors (like the ones you’ll find in CD and floppy disk drives) the motor housing is connected to the driveshaft, and both rotate together around a fixed base.
In the simplest brushless motors, a motor controller swaps power from two different coils (or two sets of coils) creating a changing magnetic field that forces the permanent magnet, and the connected drive shaft to turn. Unfortunately there is no way to control the direction this motor will start turning when you first power it. You find motors like these in applications like fish tank filter pumps, where the rotational direction of the paddle-wheel doesn’t matter, but you don’t want to make direct electrical contact to the drive shaft, since it is immersed in water.
What you have is a three-phase brushless motor. There are either just three, or three sets of coils that switch in series to lead the drive shaft in a particular direction (so your plane’s propeller won’t try to push it backwards). What you need is a special three-phase brushless motor controller. Not only will this controller generate three separate PWM signals to drive the three sets of coils separately, it will use either embedded hall-effect sensors, or more likely just measure the back-emf generated in the coils when they are not in use, to detect the position of the drive shaft magnets. It will use this information to time the switching of the coils to the rotation of the driveshaft, so the coils switch on and off at the right times. The controller will vary the duty-cycle of the three PWM signals on the fly to keep the motor turning at the commanded speed.
Brushless motors do have advantages for hobby airplanes. They are more energy efficient (lots of power is lost in the sliding brush-stator contact), they don’t overheat as easily since the coils can be in direct contact with heat-sinking elements, and three-phase motors have speed-control feedback without any special added encoder. I am not aware of any Pololu product that can control a three-phase brushless motor, but you can get a small one specifically meant for model aircraft from most hobby websites. They are usually called ESC, for electronic speed controllers, but this name also applies to speed controllers for brushed DC motors, so be careful! Astro Flight makes some ESC’s for brushless motors, and Tower Hobbies specifically “matches” the 020 with an ESC, but I’m not sure if it’s from Astro Flight or not.
Best of luck!