Hi,
Yep possible to control 2 wire fans. Can either just have them set to come on at a certain temperature, or can use PWM control to alter the fan speed based on temperature.
Fans are defined the the config.g file:
For example:
M106 P1 T45 H1
would set fan 1 to run any time the temperature of heater 1 is above 45 Celsius.
More info on fan connections here:
https://duet3d.dozuki.com/Wiki/Connecting_and_configuring_fans
And details on the m106 command here:
http://reprap.org/wiki/G-code#M106:_Fan_On
Just a note on PWM: I found my 2 wire fans were noisy with the default PWM frequency but adding in F20 (set frequency to 20Hz) to slow down the frequency at which they are turned on / off made them near silent.
Hope that helps!