I used Adafruit_neopixel and was creating the object for each LED bunch as below,
#define NUM_LEDS 3
#define C1_STRIP 8
#define C2_STRIP 12
Adafruit_NeoPixel C1(NUM_LEDS, C1_STRIP, NEO_GRB + NEO_KHZ800);
Adafruit_NeoPixel C2(NUM_LEDS, C2_STRIP, NEO_GRB + NEO_KHZ800);
and later used this C1 and C2 with fill() of the neopixel header
but this only supports Arduino cape digital pins, but I have to connect it on pin33 PE2 of the mega32u4.