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I'm not 100% sure what your question is, so my response is a bit generalized.
The original 6V system is positive ground. It matters for your generator & regulator, and for ignition system efficiency (spark jumps easier one way than the other when hotter ground vs colder ground). Everything else will work pretty much the same.
Most 12V conversions use negative ground. Again the generator & regulator (or alternator, whatever) will care which is ground, and ignition efficiency is better when the proper side of the coil is ground. Any modern electronics will probably care.