My truck came with a winch and a duel battery setup but there is no connection from the alternator and first battery and the winch and second battery.

Two things, One: how should I connect them

Two: Is the stock alternator strong enoght to run this? and if not what alternator would you recomend

I also have a bettery disconnect switch betwwen the winch and unplugged battery.

thanks for any help

Marine A, B, AB battery switch would be easy.

Stock alternator is 40-55 amps. Whether this is "enough" depends on how much winching you do.

A solid state relay (battery isolator) will work just fine. It will be a heavy draw on a stock alt when the 2nd battery is drained. But remember, you aren't running the winch off of the Alt. You are running it off of the battery. The alt just recharges the system.

That having been said, a nice upgrade is to switch to a GM one-wire alt (70+ amps).

Do I just need to wire the positives or do I need to run the grounds too. And just to be sure you run positive to positive not positive to negative or it will fry the whole thing. I thinck I learned that in 4th grade science time.

Do I just need to wire the positives or do I need to run the grounds too. And just to be sure you run positive to positive not positive to negative or it will fry the whole thing. I thinck I learned that in 4th grade science time.
The positive lead from the Alt goes to the center post of the isolator. "A" side goes to primary system (through Amp meter). "B" side goes to 2nd battery (pos).

I have the ground cables for both batteries tied to the same frame point.

Is the GM Alt a direct bolt on or will I have to get a new belt and would I just plug the wires into were the old ones are?

if you have a 79 FJ40 judging by your name you will have to do some grinding to the alternator bracket and to the actual alternator. I can take a picture of how mine is set up, I got the idea from another PBB user. For a delco alternator the wires you will have a "gen lamp" wire which will tell the alternator to start charging, a red wire that will hook up to the postive post on the alterator, and then you run the main wire to your amp meter or to the starte selonoid post. I did see the stock delco plug at Autozone. If you need pictures i'll take some after my class at 4.

a few pics would be nice, or if there is an old post describing this procedure, if you could direct me to that

http://www.pirate4x4.com/forum/showthread.php?t=281683