When working with the ports on the Linux-level, Pin Muxing are performed by MRAA library. In the case of the microcontroller it is necessary to take care with scripts...
MRAA Low Level Skeleton Library for IO Communication on GNU/Linux platforms
Configuring all 4 of the PWM pins
root@edison:~# vi pinmuxpwm.sh
#!/bin/bash
# Configuring PWM pins
# The Intel Edison SoC offers only four PWM pins.
# Setup shield pins of arduino as a PWM output
# the TRI_STATE_ALL signal is controlled by GPIO 214
# Before setting up any muxing, set pin 214 (TRI_STATE_ALL) to HIGH,
# make all of your changes, then set pin 214 to LOW.
# all GPIO pin-mux must be set to 'mode1' to select PWM
# Shield_Pin | Linux_GPIO | Output=High | Pullup_enable
# IO3 12 251 219
# IO5 13 253 221
# IO6 182 254 222
# IO9 183 257 225
#Export the relevant pins
echo 251 > /sys/class/gpio/export
echo 219 > /sys/class/gpio/export
echo 253 > /sys/class/gpio/export
echo 221 > /sys/class/gpio/export
echo 254 > /sys/class/gpio/export
echo 222 > /sys/class/gpio/export
echo 257 > /sys/class/gpio/export
echo 225 > /sys/class/gpio/export
echo 214 > /sys/class/gpio/export
echo "Exports Done"
# FIRST Shield_pinIO3
echo low > /sys/class/gpio/gpio214/direction
echo high > /sys/class/gpio/gpio251/direction
echo in > /sys/class/gpio/gpio219/direction
echo mode1 > /sys/kernel/debug/gpio_debug/gpio12/current_pinmux
echo high > /sys/class/gpio/gpio214/direction
# SECOND Shield_pinIO5
echo low > /sys/class/gpio/gpio214/direction
echo high > /sys/class/gpio/gpio253/direction
echo in > /sys/class/gpio/gpio221/direction
echo mode1 > /sys/kernel/debug/gpio_debug/gpio13/current_pinmux
echo high > /sys/class/gpio/gpio214/direction
# THIRD Shield_pinIO6
echo low > /sys/class/gpio/gpio214/direction
echo high > /sys/class/gpio/gpio254/direction
echo in > /sys/class/gpio/gpio222/direction
echo mode1 > /sys/kernel/debug/gpio_debug/gpio182/current_pinmux
echo high > /sys/class/gpio/gpio214/direction
# FOURTH Shield_pinIO9
echo low > /sys/class/gpio/gpio214/direction
echo high > /sys/class/gpio/gpio257/direction
echo in > /sys/class/gpio/gpio225/direction
echo mode1 > /sys/kernel/debug/gpio_debug/gpio183/current_pinmux
echo high > /sys/class/gpio/gpio214/direction
echo "PWM Pins Configured"
You should be able to use any of the PWM pins as output. For example pin IO6: