For building code with the NDK in Eclipse, it's really useful to make a "custom builder" for the code in your project's jni/ sub-directory.
This skips the need for an apps directory that older NDK revisions needed and with ndk-r8 (revision 8) you don't even need cygwin on a Windows machine any more. It uses the ndk-build.cmd batch file to build your code (see image above).
How to do it
Right-click your project, add a new Builder, set up your Location and Working Directory as in the image above.
For the Refresh tab, select Specific Resources, Specify Resources button, then select the libs/ sub-directory in your project.
For the Build Options tab, check Specify working set..., hit the Specify Resources button and select your jni/ sub-directory to have it rebuild whenever you change a file in the jni/ sub-directory.