I did exactly as you did several years ago, but found it a little troublesome. You will find that the alternator will have a small continuous draw on the batteries. I solved this by installing a latching relay that would open the battery circuit. You will also want to build a buss for the 2 separate voltages. Look at Blue Sea dual buss bars. They are built for the marine market but I found a simple one that worked for me. As time went on I found my 12 volt load continued to grow. Heater blower, starter, brake lights, headlights, modern radio. I still run a dual voltage system but I have gone to a 12 volt battery with a GM 10SI single wire alternator and I step down the voltage for the ignition and the remaining 6 volt system with a voltage reducer from www.koolcars.us./catalog.html . Even this system has it's limits at 20 amps. I put in a fuse ahead of the voltage reducer to keep from burning it up. I found that running the 6 volt defroster and the 6 volt wipers at the same time would overload the voltage reducer and burn it up. The fuse protects the voltage reducer now, I just have to make a decision which I need more, wipers or defroster. I don't think the operating loads are that high but both motors have a starting spike that creates the problem.