Marlin firmware V 1.1.8 / 1.1.9, RAMPS 1.4 board Configuration "EFB"
I'm also using a board known as an RRD Fan extender board.
This board plugs into the Servo port and uses pin 6 and 11.

From what I understand there are 3 fan definitions possible.

FAN_PIN seem to be used to define the D9 Pin.
While FAN1_PIN AND FAN2_PIN go undefined.

So in the "pins_RAMPS.h" file I configured the following: in V1.1.9
#if ENABLED(IS_RAMPS_EF // Hotend, Fan, Bed
#define HEATER_BED_PIN RAMPS_D8_PIN
#define FAN1_PIN 6 // DJB
#define FAN2_PIN 11
In V 1.1.8
#if ENABLED(IS_RAMPS_EF // Hotend, Fan, Bed
#define FAN_PIN RAMPS_D9_PIN
#define HEATER_BED_PIN RAMPS_D8_PIN
#define FAN1_PIN 6 // Define servo pins for fan use DJB
#define FAN2_PIN 11

In both cases FAN1_Pin works by using the M106 P1 S128 command.
But in the case of FAN2_Pin it does not work.
Using M106 P2 S128 or M42 P11 S128 does not work.

So I figure I am either misinformed about FAN2_PIN, it uses a different
command structure or I may have a bad board.

Any help would be appreciated.
thank you

This may be late but I was working through the same thing using a RAMPS derivative board (PICA Shield).

Reading through the Marlin Github issues category, it appears that only one fan is supported by Marlin. M106 P0 should be the part cooler fan.

I edited my pins file to remove my second fan that goes to the extruder.

Edited Configuration_adv.h where it says extruder cooling fans:
#define E0_AUTO_FAN_PIN 7
(mine is pin 7)

and:
#define EXTRUDER_AUTO_FAN_TEMPERATURE 15 // was 50 changed to 15
#define EXTRUDER_AUTO_FAN_SPEED 255 // == full speed

so my extruder fan is on anytime the temp is above 15 degrees C

Some also suggest just connecting extruder fan(s) to 12v so they run 100% of time.