but you cannot use the above resistors, before this would overload the arduino since it can only supply 40ma from a pin at a time and since the they are using common anode on the 5v pin.
No the 5V pin on an arduino is not a processor pin, it is connected to the power supply and is good for at least 300mA, it is only the processor's output pins that are limited to 40mA.
I thought LED's had a limit that they only activated(switched on) at, is that a Volt Level or Amp level?
Yes it is the voltage has to be at least the forward voltage of the LED.
I didn't know you could run then at lower current levels.
You can run them at what ever current level you like below the maximum, it is just that the LED gets dimmer. My last project had a blue LED in it in direct view, a current of 3mA was more than enough in that application.