I don't think there's anything like a stacking order. If you want the shirt on top of the skirt you'll have to fix this after import. Even more annoying: You might have to do this again when you change the pose.
The only way will be to resculpt the sweater in blender in such a way that it covers the skirt like it does in real life (or cover the sweater with the skirt) or remove/compress the bottom part of the sweater.
Possibly the z_depth in the .mhclo file could be changed in the related clothing items. Things closest to the body lower numbers, farther away higher. Don't remember the allowed range. This can also be set in makeclothes when creating new clothes.