Roughly:
* Write an AndroidManifest.xml.
* Write a minimal Android activity. I think you can skip this if the program doesn't need a GUI or doesn't need any of the Android APIs. I'm not sure, though.
* Write Makefile(s) to build your project. If the project does use an activity, the C++ part will act as a library that's loaded by the Java bit and main() will be called from the JNI.
* Write your code and add your files to the Makefile.
* Build your project with the NDK, separately from the IDE.
* Deploy from the IDE (can also be done directly from command line using ADB.
The easiest way is to start from a skeleton project that you can modify to you needs. My project used SDL2, which provides such a skeleton.
You can take a look:
https://github.com/Helios-vmg/CopperRat
The main source is under src/jni/src
Beyond the initial setup, most things are relatively straightforward. The C++11 compilers are feature-complete, but the standard library still somewhere between C++98 and C++11. My project even builds on both Windows and Android with very few platform-specific sections.
For questions specifically about Android development, you may have better luck at XDA Developers:
http://forum.xda-developers.com/android/software