XMEGA384C3 PORTA digital IO
On the XMEGA384C3, is it possible to use PORT A and PORT B for General IO digital pins? 


Yes.


  On the datasheet it saids that the pins are for analog only.


You have misunderstood the ATxmega384C3 datasheet :-) However I can see how it could be interpreted the way you said e.g. the pinout diagram in section 2.

Pins on PORT A or PORT B can optionally be used for connections to the MCU ADC module (they are the only ports which can, optionally, be used for ADC measurements). That doesn't change the fact that those ports can also be used for standard, digital GPIO.