The reason your bass is worse than the stock speakers is cause the MBQs' crossover cuts off the lower frequencies. Aftermarket components are usually designed to be supplemented with a sub, whereas stock speakers are not (they typically play full range).
In tuning it, first decide where your speakers are lacking (highs too harsh, midbass is lacking, midrange isn't defined enough). Work with the crossover slopes, the width of the bands, the crossover points, etc...