Tap into the freezers incoming power to also supply the STC-1000 with power (terminals 1&2). Remove the two wires going to the freezer thermostat, and move them to the two poles of the cooling side switch on the STC-1000 (terminals 7&8). Wire the temp probe to terminals 2&3 as normal. To add heating, run an additional hot to one leg of the heat switch in the controller, then from the other side of that switch to the heater, and then a neutral to the heater.
I'm not sure that this is any more elegant than running wires from the controller to a single gang box mounted somewhere out of the way (like in the back of the collar) and simply plugging the freezer and heater into that, but that's how you'd incorporate it into the freezers wiring.
FWIW I wired mine just like the ones you see in a project box, but my controller is mounted in the collar, and the duplex outlet is mounted in a single gang box that I put out of the way in the compressor area.