2 arduinos, 6 relays and usb power supply

I'm guessing that when you have only one USB cable plugged in you get a notice that your USB port has been shut down because you were drawing more than 500 mA. If it works OK with BOTH USB cables plugged in you are probably drawing less than 1A total. If that's the case you can connect a 5V 1A regulated power supply to everything to take the load off your USB ports.