You should use the fullfile function to create the filepath. Your call to imwrite function is in the outer for loop, hence it will only save once per outer loop. You should call it in the inner loop to save all. Also to avoid overwriting the files, you need both i and j values in the filename.
dirtosave = 'C:\mydir\';
for i=1:n
....
for j=1:m
A=myfunction(...);
fname = sprintf('A_i_%i_j_%i.png',i,j);
imwrite(A,fullfile(dirtosave,fname));
end
end
