Without reading the docs for that model myself I'll guess no. And here is why. Generally a two stage controller lets you set two temps, one is a upper limit and the other is a lower limit. When the temperature rises past your upper limit the cooling circuit gets powered. When the temperature drops below the other the heating circuit gets power.
Point me to a link to your spec sheet and I'll take a look.
I agree with camiller but will add that I think the draw of both frezzers being on at the same time (if that's even possible) might prove to be too much for a single controller to handle. Also, is it possible to wire two thermometer probes into it?
Looking at the doc BK linked it dies look like it could work since each "stage" can be set to heat or cool but.... the combined amperage of two freezers might overload it, or the house circuit it is hooked up to. C2 is limited to 8 amps while c1 can go to 16 amps. The biggest concern would be the unlikely (but eventual) instance where both freezers kick on at the same time.
The amperage overload was my main concern so I'll probably not attempt 2 freezers. I may pursue a freezer and fermentation chamber using fan and ducts to pull cool air from the freezer to the chamber controlled by one stage and freezer control with the other stage.
I think it has more to do with the amp load from your freezers compressor. My little 5.5 cubic foot freezer only draws around 2 amps at full load. Camiller is correct; each output from the controller can be set normally open or normally closed. I believe all you would need to have are two temp probes and get all of the parameters correct.