So where it says atmosphere cfw. That's the entry you were talking bout. So that entry is chainloading fusee.bin (the "official" way to boot atmosphere) this method is exactly similar to booting hekate select chainload. Then choosing fusee.bin
As for wether your booting into emunand or not. Fusee.bin will automatically choose for you if you have an emunand and it's enabled. (You should be able to check if it's enabled in hekate). Ultimately you won't know 10000% wether you are or not the first time you boot up. After booting it up go to settings, system update. And under where it says update now it'll show a string of numbers and letters.
For example: 15.0.1|1.5.3|E
The first set is the firmware version your on. The next set is what atmosphere version your on. While the ending letter let's you know wether your in emunand or sysnand (s=sysnand, e=emunand)