You need to write on yourself, or use Eclipse to create a project, or use the android sdk command line tool to create a project...
but my question remains... If you only have native code, how are you going to make the user interface?
You need an activity, (native or not).
so to summarize...
You need FIRST to create a standard android project (using eclipse, or cmd-line tools)
then, create the jni folder and drop in your code (you'll also need to create an Android.mk file to tell ndk how to build your shared library)
My feeling is that you are not ready to build a project using NDK (don't take it personnaly, it's just the feeling I have reading your questions)
My advice is: try first to create simple android apps, (without using NDK... NDK add alot of complexity to an android application, it's not just "compile and run", you need also to managed the Java -> C binding and C -> Java binding using JNI)
learn how to build the AndroidManifest.xml (it's not that difficult), eclipse can help you with a GUI, but usually I'm writing it with the Text Editor (refer to Android SDK)