If you are mounting it into a shutter, why would you bother using the stops? I suppose they might give you a perfectly round 'bokeh', which might be nice, but otherwise I can't see any possible advantage...
In any case, it is easy enough to use waterhouse stops, just make sure they are centered and seated properly. Many waterhouse stops have a slightly beveled edge, I *think* that these are supposed to face the film-side. Exposed metal on the stops can cause flare, so make sure they are all painted.