I am using a KFB2.0 3D printer controller board which is ramps 1.4 I was having the same issue for where I had to have my extruder 2 hooked to my fan port to use the second extruder. I have found out that if you change in pins.h for the ramps 1.3 where it says Heater_2_pin 9 to Heater_2_pin 7 then you can use the fan and the second heater they way it's suppose to work I was wondering if there is any way there can be a ramps 1.4 added to the pins.h with this change in it or atleast for the KFB2.0 board.
// uncomment one of the following lines for RAMPS v1.3 or v1.0, comment both for v1.2 or 1.1
#define RAMPS_V_1_3
// #define RAMPS_V_1_0
#ifdef RAMPS_V_1_3
#define ORIG_X_STEP_PIN 54
#define ORIG_X_DIR_PIN 55
#define ORIG_X_ENABLE_PIN 38
#define ORIG_X_MIN_PIN 3
#define ORIG_X_MAX_PIN 2
#define ORIG_Y_STEP_PIN 60
#define ORIG_Y_DIR_PIN 61
#define ORIG_Y_ENABLE_PIN 56
#define ORIG_Y_MIN_PIN 14
#define ORIG_Y_MAX_PIN 15
#define ORIG_Z_STEP_PIN 46
#define ORIG_Z_DIR_PIN 48
#define ORIG_Z_ENABLE_PIN 62
#define ORIG_Z_MIN_PIN 18
#define ORIG_Z_MAX_PIN 19
#define ORIG_E0_STEP_PIN 26
#define ORIG_E0_DIR_PIN 28
#define ORIG_E0_ENABLE_PIN 24
#define ORIG_E1_STEP_PIN 36
#define ORIG_E1_DIR_PIN 34
#define ORIG_E1_ENABLE_PIN 30
#define SDPOWER -1
#define SDSS 53
#define ORIG_SDCARDDETECT 49
#define LED_PIN 13
#define ORIG_FAN_PIN 9
#define ORIG_PS_ON_PIN 12
#define HEATER_0_PIN 10
#define HEATER_1_PIN 8
#define HEATER_2_PIN 7 // changed to 7 from 9 to make heater work.
// ANALOG NUMBERING
#define TEMP_0_PIN 13
#define TEMP_1_PIN 14
#define TEMP_2_PIN 15
#define E0_PINS ORIG_E0_STEP_PIN,ORIG_E0_DIR_PIN,ORIG_E0_ENABLE_PIN,
#define E1_PINS ORIG_E1_STEP_PIN,ORIG_E1_DIR_PIN,ORIG_E1_ENABLE_PIN,