generally I would think this should be taken care of firmware-side by the manufacturer, but there is G-Code you can use to change the offset.
Put in your starting Script:
What this will do is set T0 as the 0,0 point, and then set T1 offset in relation to the T0, so measure how far away the second nozzle is from the first nozzle on the XY plane, and replace the 20 (used as an example) with your specific offset. It's a good idea to keep this in the starting G-Code so that anytime you start a print these offsets will be loaded.
Have not tested, but you may be able to use the Machine Control Panel, send in those lines 1 by 1, then use the M500 command to save the offsets to the eeprom of the microcontroller. If this works, you won't need to use the M218 command everytime and should be saved even with a power-cycle of the printer. Some firmwares will allow you to use the command M503 to read the EEPROM stored values.