You didn't show the code used to create the plot but the answer in general is to first save the handles to the two axes so you can subsequently modify them...
hAx=plotyy(x1,y1,x2,y2); % a 2-axes plot; save axes handles
ylim(hAx(1),[LftLoY LftHiY]) % invoke ylim() on LH axes
ylim(hAx(2),[RtLoY RtHiY]) % and RH
If you have more recent release, TMW recommends yyplot instead; it makes control of such elements a little more easily managed...
