I hope you're not using all three filters at once!? I saw just that recently with a strictly geekish type carrying a monster Canon and three filters stacked on the end of an L-series lens (!).

Anyways, slight over- and under-expose of transparency e.g. either through push or pull (post-exposure; this is essentially a compromise and not a universal fix for bad exposure decisions) or in-camera (exposure compensation or exposure indexing iso 100 treated as e.g. iso 80 (+0.3) ) can work wonders in specific situations. This, like everything else, will come down to experience, and it's a wonderful teacher.