Connecting the battery 'backwards' almost always 'fries' the alternator the moment you turn the ignition ON and try to start the engine...!
The output diodes built into the alternator usually can't handle the high current surge, along with other unwanted bits being fried as well...
It's probably best to remove the alternator and take it to an automotive electrical shop than knows about this stuff - not necessarily your corner chain type auto parts store (IMHO most of them don't know up from down when to auto electronic stuff!)...check your phone book for a 're-builder' type shop...they deal with this stuff every day!
You've figured out the error of your ways...however, I always tell customers to look at the two 6 volt batteries as being, in essence, one BIG 12 volt battery - as such you have to have a HOT (pos) connection and a GROUND (neg) connection to hook to your vehicle - that being said, in effect demands that the other two terminals on the batteries must be hooked to each other (SERIES type connection) to complete the circuit - also - NO OTHER CONNECTIONS are made to these two series connections!!!!
It's rather easy to hook up 6 volt batteries 'backwards' as the terminals are on opposite corners, and the battery could be turned end-for-end and appears the 'same' - a closer look will show that the POS terminal is ALWAYS larger in diameter than the NEG terminal (also true on 12 V batt's), as an aid to making the correct connections - the POS cable opening being larger, is usually a LOOSE fit if you try to put it on the NEG terminal, etc., etc....when using 'eye' cable connectors on a GC battery, you're sunk, as the cable will fit on either 5/16 inch stud connector - look carefully at the + or - marks next to the terminals to make the correct connection...
Good luck,
Ray
Ray