In general if you return handles to your figures/axes when you create them, you can tailor each piece by passing that handle as the first argument to a plot modifying function.
So if you did
a1 = subplot(2,1,1);
a2 = subplot(2,1,2);
you could then do
xlabel(a1, 'title here', 'FontSize', 12)
xlabel(a2, 'other title', 'FontWeight', 'bold')
or any other label-specific customizations you want.