I agree completely with what Rob says about when and where to apply the smaller piece of glass. However, I would like to put some bounds on it. If you can place the smaller piece under the bigger piece and not create a situation where you will potentially sand through the glass, then you can do it.

For example, some of my designs have a fairly sharp chine. If the edge of the smaller glass is along this sharp curve, the transition between the layer thicknesses becomes part of the chine. Here you can make a smooth curve without out sanding into the top layer.

Ather option is if you don't really care about making a perfectly smooth surface and just want to save some time and effort, you will get a smoother surface without sanding with the smaller piece underneath. You won't get those annoying loose strands. Just don't sand much and live with the transition lump.

If you don't mind the extra weight of building up with epoxy, you can always fair the transition by filling with additional resin.

But in general - smaller layer on top is "better".

: A second below the water layer of glass must be added over the full hull
: layer. This allows the edge of the second smaller layer to be feathered
: (sanded smooth) with the previous one. Whenever you will sand a surface
: the additional layer MUST be added on top. IF you put a smaller piece of
: glass under a larger layer of cloth a step down in the surface will be
: created at the edge of the partial layer. If you sand this edge you will
: cut through the full layer of cloth and destroy the integrity of the hull
: strength.