When running two batteries I like using a Batery Isolator. Your alternator will keep both bateries charged but you use the 2nd for your winch and other assessories. Also if your main batery goes dead you can jump yourself <img src="/forums/images/graemlins/lol.gif" alt="" /> <img src="/forums/images/graemlins/lol.gif" alt="" />. If you had your old alternator rebuilt to 110 Amps it would keep both bateries charged (above idle) better. A good place to mount the 2nd battery would be to make a air snorkel and use the spot that the air filters is now.
Dennis