Yep. Bare in mind that having a 2007 you already have a slightly bigger alternator than all of the other JKs. But, if you want to go really big, check out this one ...

amazon.com/Mean-Green-07-10-Wrangler-Alternator/dp/B004KU1U78

As for the second battery, as others have stated it is a back-up. If you off-road, especially expedition/overland type travel on washboard roads for long distances (as opposed to rock crawling or mudding or mall crawling), then the vibrations are battery killers. During a 150+ miles trip through the Arkansas Ozarks late last year, four JKs and two had battery problems. One didn't have dual batteries and it took two Jeeps to get him cranked. Even after that, the Jeep kept flashing warning lights and other weird stuff until we got into a town and replaced his battery. On my Jeep, I just pressed the boost button on the battery isolator, cranked, and went about my business until the trip was over and I could replace the dead battery.