I had the idea of staying with 6 volts on a future project that will most likely be around a Y block so just how much more compression over stock can a 6 volt system take,if its not much then I think I might just forget that idea of staying with 6 volts as I do not want to have problems starting mainly when at operating temps.
Its is not the volts that crank the motor, its the amps. If you have appropriate cranking amps and a starter stout enough to spin the motor then you can start anything with a 6V battery that you can a 12V battery. On a street driven vehicle with iron heads you are not going much past 10:1, your 6V system in good shape should handle that just fine.
Look for a 6V battery and starter that will provide higher CCA. There should be a combination that beats stock specs. If not, go 12V.
The most important thing with a 6 volt systems is proper size battery cables. 12 volt cables will not work well with a 6 volt system. Positive or negative ground makes no difference. make sure both cables are in the 00 range.