Look in the platform-conf.h in eg contiki/platform/sky/. There you'll find the definitions you can use, of eg LEDS_RED.
Then, in your application,
#include "leds.h"
...
leds_on(LEDS_RED);
leds_off(LEDS_GREEN);
leds_toggle(LEDS_RED);
leds_off(LEDS_ALL);
You can look in leds-arch.h to see how the implementations sets/get LED state.