You will have to write code that changes the use of the pin depending on your jumper. My suggestion is to make two configurations (builds) of your project. Each copy will be configured for one of the two specific uses alone. That way you can test that they both work independently. AND even more importantly, you can compare the PE generated code for each build and find see how the PE tool configures the pin and peripherals for each output. (use a freeware tool like Diffmerge to compare the code files in each project directory)
Once you do that, you can make a single project that can run the appropriate configuration code depending on which use you want for PTB3.
In general, you need to do two different things to switch from ADC input to GPIO output. I am using MCUExpresso and the latest Kinteis SDKs, not Processor Expert. So this is purely example code, but I expect that the solution for your situation will be similar. (BTW, Why are you using old tools like PE? I suggest updating to the current toolchain if you want to get the best help on here.)
1: Initialize the pin as an output, with an initial state of 0:
gpio_pin_config_t gpiob_pin38_config = {
.pinDirection = kGPIO_DigitalOutput,
.outputLogic = 0U
};
GPIO_PinInit(GPIOB, 3U, &gpiob_pin38_config);
2: Switch the pin MUX to GPIO, this disconnects the port from the ADC and connects it to the GPIO module:
PORT_SetPinMux(PORTB, 3U, kPORT_MuxAsGpio);
If you wanted to switch back to ADC, you would need to do a similar thing, except set the pin mux to ADC instead of GPIO:
(PORT_SetPinMux(PORTB, 3U, kPORT_PinDisabledOrAnalog);
