I would suggest calling your Allen Bradley rep to help you select the correct method. You may also want to consider using the high speed counter cards for a slc500. The slc cards should be a cheaper solution.
If you need more help let me know.
You probably have a eeprom installed and need to save your changes to the eeprom. If you do not want the program to load from the eeprom you can disable the Memory Module Loaded on Boot S:5/8 in the processor status file.
I am assume that the controller is a slc5/03 or newer. The above info...