You can position them yourself (or programatically) using
subplot('Position',[left bottom width height]);
By default, the coordinates are normalized. So a position
of [0.1 0.1 0.5 0.5] will start at 10% of the way in
from the lower left corner, and will have a width equal
to half the figure width, and a height equal to half the
figure height.
See the accepted answer for a built-in solution to margins and padding.