I agree with Stephen, if you leave the two polarizers in then you will have a homemade variable ND filter. If you just want the polarizing effect, then unscrew the base filter and go with your nicer one. When using the separate polarizer, there should not be a difference with vignetting with the inner filter installed or removed. But it is possible that you will have less vignetting if you use the built-in polarizer alone, and not the separate polarizer, because the separate one sits a little bit farther away from the lens.