do a little searching, I know SeanP has an Atlas in his, and I think Jes does as well. I seem to remember SeanP cutting some of the floorboard, but that may not be neccesary if you clock it lower. the front driveshaft will probably still work, but the rear will probably need to be lengthened. you may need some sort of clocking ring/spacer to bolt it to the AX15. and the skid plate might need a little adapting.
also do a search on www.pirate4x4.com/forum/search.php? there are a lot of YJ guys with the AX15 and Atlas, and some of the same things will apply.