Dunno about your equalizer in particular but here's my thoughts on equalizers in general.
You're using it correctly by using it mainly to cut rather than boost. People get in trouble when they go for the infamous "smiley face" configuration in order to boost the frequency extremes, which can suck an amplifier dry,
As for any increase in distortion, can you hear it? If not, then you're worrying needlessly.
Ultimately, here's the question you should be asking yourself: Does my system sound better with it or without it?