Your question leaves out a lot of details.
What did you connect to the Navio?
With PWM a 1500us puls is usually center for servos.
An aircraft ESC uses the whole PWM range (ca. 1000 -2000us) to control throttle in one direction.
A car ESC turns a motor in both directions, below 1500us backwards, above 1500us forwards.
You can not vary the output voltage of tbe Navios servo pins. The voltage is 5V and thats it.
The only way to control anything from the servo pins, is the PWM signal on the signal pin.
Sorry, my smartphone did not load the link you posted. If this is an h-bridge based motor controller, you may have to send it some kind of a signal to switch directions. It should be described in the controllers manual.
I looked at the datasheet of the controller and to use it you will have to connect 6 control inputs (3 per motor). AIN1 and 2 (or BIN for the other motor)
must be set high or low to achieve braking and reversing. This will be hard to do with RPi and Navio attached. The way I would do it, is to put a microcontroller (arduino for example) between navio and the motor controller. It would convert the PWM range from the Navio to the inputs required by the motor controller.