jake53,
I am not sure I understand what you are saying, or asking. It sounds like you swapped a 12 volt battery for a 6 volt...unless you did a whole bunch more your parade days are numbered.
To my knowledge your truck would have been NEG ground. The ammeter is polarity sensitive, so if the system is actually operating correctly, the leads on the back of a ammeter gauge would be swapped in order to get it to read properly.
I am guessing you have left out a lot of what you have done in your explanation above!
Stuart