Hi Cagri,
1) What do you mean by "USB-CONSOLE" exactly? I guess you would like to use a Serial Console on a CDC ACM (serial communication) USB function. This is implemented by default with the later images, just connect the board to your host and a CDC ACM device should appear. On Linux, you can use the TTY /dev/ttyACMX to connect to it.
2) The two cores share the complete peripheral bus, hence all GPIO's are available from both cores. However, you should make sure that each GPIO is only assigned to one core (or even better, a complete bank of GPIO's). What kind of firmware are you planning to use on the M4 core?
--
Stefan