what guage wire to run from my alt to perko
 

I'm installing my second battery and perko switch. I want to run a wire from the alt to the perko. I have no idea what guage wire I should use.
100amp alt.
2 gauge runing from starter to battery and grounds.
running 2 amps, WS SYN 6 and the stock clarion that runs the sub and boat speakers.
ballast pumps.

Are you asking about the two 'field wires' between the alternator & perko?
I don't think it really matters much, there will not really be any amperage passing thru them, just voltage.
I think I used 16 gauge on mine.

Assuming your perko switch is up towards the front in the passenger storage compartment of the boat I would run 0/2 awg wire from alt to perko for 100 amps.

So are you running the starter cables to the battery but another cable from the alternator to the perko? I think you need to go about this a little different. I would move the positive that goes to the starter from the starter battery to the common on the perko. Then run a 1 or 2 gauge wire from the alternator to the common terminal as well. In this combination you are basically using your combined wire to charge. Remeber that you may need to upgrade your ground cable as well but considering that it is probably 2/0 already running from the batteries to the block you may be fine. I have a chart somewhere that show what size cable depending on length of run and amperage. for a 24 foot combined run(both positive and negative) at 100 amps you can get by with 1 gauge. As your system is setup from the boat manufacturer you are only utilizing the small(probably 8 gauge or so) from the alternator to the circuit breaker. The other thing you could do if you do have 2/0 or 1/0 battery cables from teh starter is make a 1 gauge cable that goes from the alternator to the starter positive. The only problem is it may be tough to fit 2 lugs on the positive stud of that starter and alternator.

basically i want the alternator to charge whatever battery i have selected. I'm running the stereo off battery 2 and the starter off battery 1. So say, if I run down battery 2 while parked partying, when I switch to battery 1 to drive home, my alternator won't die trying to charge battery 2. I have an on-board charger to charge when I get back to the dock.