The UART module can use RTS and CTS automatically. You just enable the functionality. Example for this is given in MQX:
_bsp_serial_io_init() function in gpio_init.c to enable pin functions.
_mcf52xx_uart_serial_polled_ioctl(), case IO_IOCTL_SERIAL_SET_FLAGS, to enable transmitter CTS checking and receiver RTS assertion/deassertion.