Good, you must not pass all that current though any Arduino board. The PCB tracks on Arduino boards are not designed for such high currents.
On the subject of current, your 2 matrices will probably draw up to 0.5A in total even with every led off. The chips inside each led need around 0.5~1mA each. If you light 1 in 4 LEDs in blue at half maximum brightness, I guess that would be around 1.8A.