I know for a fact that the EVB9S12NE64 is built to support the HCS12 Serial Monitor program that is directly supported by the free version of CodeWarrior for HCS12s V3.1 Special Edition. The Serial Monitor is a program that resides in Flash memory that allows you to program/erase RAM and Flash and read/write other internal memories via serial cable between PC and board. Look at AN2548 for more information on the HCS12 Serial Monitor. Also, AN2548SW1 and AN2548SW2 include the software.
You know, I also suggest sending Axiom Manufacturing (www.axman.com) and email to find out if they have an updated AXEIDE and monitor that supports the NE64.