Awesome! Thanks for the hint Traumflug. Here's what I did:
I uncommented DEFINE_HEATER(fan, PORTB, PINB5, OCROC) and changed it to DEFINE_HEATER(fan,AIO2) (because my heater is connected to analog pin 2) then below I uncommented #define HEATER_FAN HEATER_fan
And now it works! Of course I had to connect the fan pin to my sanguino mainboard at analog 2. It would be nice if it worked with the seperate extruder controller, but I guess that's my fault for sticking with obsolete electronics (and being too lazy to rewire everything).