It's difficult to understand exactly what you want to do from your question, but the way poly stippling in gl works is basically this: you can enable polygon stippling and supply a 32x32 pattern that is used to control the stippling. It is as if this pattern were tiled over the entire window you are drawing to. Polygon fragments that fall on pixels (in window coordinates) that the stippling pattern says should be masked are not sent any further in the gl pipeline (so those polygon fragments are not drawn.)
I'm not sure what it is you are trying to do though- if you could clarify that I might be able to give you a more specific answer.