ignition and charging system question

[mean715]

I was wandering if there was an easy way of telling if the ignition system and charging system have already been switched over to twelve volts? I havent really looked over the ignition system all that well but the altenator on my jeep looks like just a regular chevy altenator. When I first got it my first goal was to get it to turn over, after trying with two batteries run in parallel the starter wouldnt even turn the engine over (it sounded like the batteries were dead). I then tried running the batteries in series, it sounds like it is turning the engine over with the spark plugs out of it (turns over very fast). Is this normal? The wiring harnass was pretty much useless from dry rot and some dummy wire nutting all the connections together, I rewired the truck and of course was so anxious and in a hurry I didnt bother to look the way the 2 systems were already ran! I dont think that it would of been wired right to begin with because the batteries were already ran in parallel for the starting system when I got it. The way I ran the starting and ignition systems was that I ran the batteries and pulled 24 volts for the ignition system (two batteries in series) and then pulled 12 volts off of one of the batteries for all of my lights and accesories. My next question was, will the polarity of the batteries ever change over time? (the posative and negative in the middle become obsolete)