Playing sound in left and right speaker alternatively and storing output in array in matlab
If you want to play only one channel then you must set zeros at one of your matrix columns, i.e.:

sound_L = sound_array;
sound_L(:,2) = 0;

sound_R = sound_array;
sound_R(:,1) = 0;


So your code becomes:

Fs = 44100;
N = 400
t = (1:N)*(1/Fs);
freq = 600;

sound_array = zeros(N,2);
%starts N x 2 matrix
sound_array(:,1) = sin(2*pi*freq*t);
sound_array(:,2) = sin(2*pi*freq*t);

%Left and Right channels

sound_L = sound_array;
sound_L(:,2) = 0;
sound_R = sound_array;
sound_R(:,1) = 0;  

%Sound 1 
sound(sound_L, Fs);
%Sound 2
sound(sound_R, Fs);
%Play Consecutive
sound(sound_array, Fs);