You run it into the cowl righ under the intake in the cowl. Spectre has a intake kit or you can make one yourself. People have used a variety of filter boxes from other vehicles such as Ford Windstar, Buick and others. I don't remember if there are threads here but jeepforum.com has a lot of build it yourself threads.
2003 TJ, 33" BFG AT, 2" BL, 2" BDS spring lift, Truck Lite headlights, Homemade sunrider top.