When I used one a long time ago, I just placed the trolling motor control in high (this should be straight through with no resistance added), and used the PWM to adjust motor speed. You shouldn't have to remove the factory switch, unless it is already a digital motor, it should just be a variable resistor, with highest speed being no resistance, just on/off. It will work fine in the lower speeds as well, but the double speed reduction is redundant.

You may have had the leads reversed, that would be a dead short across the PWM controller.