George,
Yes, if you have multiple systems, you have to identify the conductors by system, but the code does not specify how they are identified. If you choose to use black, red, blue for one system and black, red, blue with a tape mark you are in compliance with the code. The method is left totally up to the installer and the inspector has no say in it. The only other requirement is that the method of identification used be posted at every panel. Using the same color for ungrounded conductors or both systems without any other marking would be a violation. Note that under the 2005 code the required identification is only by system and not by phase so you could use all black for one system and all red for the other system. This will be corrected in the 2008 code.