Main problem with eclipse/android is that it is hard to debug C++ code because of JNI.
So most popular way for all cross-platform C++ development - including cocos2dx - is use Xcode/VisualStudio for development, testing, debugging with breakpoints etc... everything works without needing any setup. Then use eclipse or console or build/run/test on Android. It is much more easy to debug problems in Xcode/VisualStudio as C++ breakpoints work.
On Android/JNI, it is hard to setup C++ debugging using breakpoints. It is possible but difficult to setup, so only debug Android bugs using eclipse but use Xcode or Visual Studio for main development.