I'm no expert on this, but Charlieplexing is a dynamic function.
It is intended to control leds INDIVIDUALLY by pulsing them ON when required.
For two (or more) leds to be ON 'at the same time' - eg. for traffic lights - they are actually being switched ON then OFF individually rapidly. So they 'look' as if they are on at the same time due to persistance of vision.
It looks as if what you are trying to do isn't strictly Charlieplexing....
For software and examples, refer to the library :-http://arduino.cc/playground/Code/Charlieplex
For 6 leds, you only require 3 outputs.
Your green leds should be connected between 'ledpinA' and ledpinC
For your hardware, make these basic tests on the leds.
Assumiming a 5V supply and limited Arduino output current to 20mA.
Nominal forward voltages.
Red led Vf = 1.8V
Green/yellow led Vf = 2.2V
This equates to 160R and 140R resistors.
So for a test, use a standard value 150R resistor to supply one colour led individually from a 5V supply.
Note the brightness.
Are the colours similar (acceptable) in intensity?
No. -> You're stuffed until you find some that are.
Yes. -> Continue.
Because each output pin is used as a source and sink (5V supply and 0V) during Charliplexing, each output pin needs a resistor in series with it.
Using a 75R resistor in each output gives a 150R (for a nominal 20mA) total resistance.
because at any one time:-
One output will be ON (+5V).
One output will be OFF (0V).
All the others will be in input mode. (High resistance).
Hope this helps.