Unfortunately, yes, we do need neko to be in a specific place. You can see the paths Stencyl expects in the file Stencyl/plaf/install_neko.
The binaries aren't really a big deal, we just put them where the official neko installer does iirc. But because of some security restrictions with DYLD_LIBRARY_PATH on Mac, we do have to have libneko.dylib in /usr/local/lib (or theoretically somewhere else where it would be found, but again, we just went with where the official installer puts it).
Stencyl sets all the environment variables it needs to in order to ensure you have the correct setup (and not using, say, your own set of haxelibs and a different version of Haxe). This includes NEKOPATH and NEKO_INSTPATH.