Z, what you've reported is puzzling, since setting the EP500 to a crossover frequency rather than bypass can only decrease, not increase, the bass output of the sub. Also, if you mean the setting for having the sub play both the LFE bass and the low bass from the LR mains(with the mains also playing the low bass), that setting only applies when the mains are set "large", and you said that all of your speakers were set "small".
The basic suggestion is still all speakers "small", sub "yes" with internal crossover bypassed, and all crossovers in the 990 at 80Hz.
