When you use make the idea is you have a Makefile that you start the building off with. With ndk-build it according to the docs just runs $GNUMAKE -f <ndk>/build/core/build-local.mk but like is there a file in my project I need to have or what files is is looking for.
Yes, typically it expects to find your project makefile as jni/Android.mk, but you have lots of freedom if you need.