Yes, that is absolutely possible.
First of all, make sure the fan pins are defined in printer.cfg like so:
[fan_generic fan2] # auxiliary fan
pin: PB0
max_power: 1.0
[fan_generic fan3] # exhaust fan
pin: PE11
max_power: 1.0
alternatively, if you are using the DKEU macros add-on, printer.cfg should look like so:
[fan_generic fan2]
pin: PE11
tachometer_pin: PE13
tachometer_ppr: 1
tachometer_poll_interval: 0.0075
max_power: 1.0
[fan_generic fan3]
pin: PB0
tachometer_pin: PB1
tachometer_ppr: 1
tachometer_poll_interval: 0.0075
max_power: 1.0
in Mainsail you should now see Fan 2 (intake fan) and Fan 3 (exhaust fan) under the Miscellaneous tab, where you can change them manually. (and if you have DKEU, you will also see the tachometer values there).
But for the real magic, control them via Orca Slicer’s Filament Advanced G-code boxes. As an example I set mine to gently exhaust air while printing ASA or ABS, preventing fumes from escaping without significantly cooling the chamber. Then when the print is done, I retract the filament slightly, move the extruder out of the way and run both fans on high for one minute to purge any fumes from the chamber before shutting things down. To do so, my “Filament start G-code” is:
; Filament gcode
SET_FAN_SPEED FAN=fan2 SPEED=.06
SET_FAN_SPEED FAN=fan3 SPEED=0.0
and my “Filament end G-code” is:
; filament end gcode
SET_FAN_SPEED FAN=fan2 SPEED=1
SET_FAN_SPEED FAN=fan3 SPEED=1
G91
G1 E-2 Z0.2 F2400
G90
G0 X5 Y495 F12000
G4 P60000
SET_FAN_SPEED FAN=fan2 SPEED=0.0
SET_FAN_SPEED FAN=fan3 SPEED=0.0
I use similar code with PLA filaments to run both fans @ 35% (ie: SPEED = 0.35) while printing then shut them down after so I can keep the doors closed without any heat build-up. (One of these days I’ll add a chamber thermistor for more precise control but this seems to be a good value for my ambient room temperatures.)