You can control the position of a composite laminate or stack relative to its surface. You need not account for clearance between surfaces with different shell thicknesses in the geometry if you select the relevant option. The Shell Definition PropertyManager for composites has these following options:
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Middle Surface
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Positions the middle of the stack on the surface body.
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Top Surface
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Positions the top of the stack on the surface body.
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Bottom Surface
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Positions the bottom of the stack on the surface body.
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Specify Ratio
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Positions the portion of the stack defined by an offset value that is a fraction of the total thickness measured from the mid-surface to the reference surface. The figure depicts the negative and positive offset values. 
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For example, consider a hollow stepped shaft made of two different composite stacks.
You create two surfaces using the inner radius of the shaft and select the Bottom Surface option. This eliminates the need to redefine the geometry every time you change the number of layers or thickness of the laminates.