I think you're missing the point of the clipping. There's a maximum output that the empeg can produce. Call it 5V. If you tell it to produce a greater output than that, by, for example, having a track that has 100% amplitude and playing it at +2dB, it simply won't produce an output that loud. So instead of having a nice curve that goes up and comes back down, it produces a curve that has a flat top. This sounds bad, and actually causes more power to go through your speakers than you had your system set up for, potentially blowing them out.

That being said, I don't know how modifying the EQ plays into that. I don't know if it means that any band over the peak would cause problems or if the average being over the peak would cause problems, or if it wouldn't be an average, but weighted. It's possible that having positive EQ settings can cause clipping, but perhaps not to the point of prodicing too much power. I don't think that's right, though. If you had a track that was a simple sine wave and the EQ at that point was set too high, it could produce too much power, depsite the fact that the rest of the EQ bands were set way down, since they wouldn't be affecting the output much, if at all.