The easiest way is to set the properties in build.gradle:
sourceSets.main.jni.srcDirs = [] // now, AS will not try to compile your source files
sourceSets.main.jniLibs.srcDirs = ['libs'] // now, AS will pick up the compiled SO files from libs (where ndk-build will normally put them)
I also love the hack by
@sherpya: instead of hiding the jni.srcDirs, you can disable compile*Ndk tasks. The advantage of this approach is that AS lets you see and edit easily your CPP files.
Enjoy,
Alex