drained battery

whats up all i am new here first post. i recently purchased a m1009 and am having some issues with it. I accidently touched pos and neg. on one of the batteries last week and after that noticed the volt gauge was in the yellow. It later died on me that day at the store and I bought 2 new batteries because i didnt know how old they were. after replacing them the gauge was still in the yellow. it has been fine for driving in the daytime but last night I was driving it and i guess using the lights drained the juice too much and the meter went into the red and lights got really dim and would not start without a jump.
I dont have any auto electrical knowledge but do have a voltmeter and checked the batteries the rear one was fine with 12.80 bit the front battery was way down.
I have not taken alternators off yet to test but am going to this weekend.

any help would be greatly appreciated. oh also when driving and applying the brakes i noticed the gen 2 light flashing for a second. it would also do this sometimes with the turn signal.
which alternator is the #2 by the way?
thanks again in advance and the avatar is ED209 from robocop if anyone is wondering.......