Energy of audio signal From audio file [y,FS]=something.wav

So the y is typically N cross 2 matrix 

I want calculate energy so i.e  sum(abs(y.^2))

So when I apply these I end with two answer for each column. So I want only one energy for whole signal what to do???
That really depends on what you need to use the energy for and how exactly you define "energy" in your application.

You can either take the sum of the energies or do a more advanced mode taking into account the inter-channel correlation and the spectral correlation of stereo playback. If you want anything like "physical" energy, you need a calibration.