Stencil Buffer and clipping plane.

I’m using the stencil buffer to “Cap” Spheres that have been sliced using two seperate clipping planes to give a cross section of the sphere. The stencil function fills with all zero’s, turns to ones wherever a sphere is drawn, draws a quad across the screen of the cap color, then draws another sphere to cover the sections of the sphere that were not sliced. My Question is whether or not the stencil buffer will draw a color on the screen if what it was drawn over was cut by the Clipping plane if that makes sense. Because the caps are only coming on sections of the spheres that still draw (are not sliced) and I was thinking that might be the reason.