The EB-O only has a single pickup, right near the neck which makes it very bassy, dub-like and sometimes muddy, and can struggle to be articulate. I would try cutting out some of the lows to clean it up. You might also want to try plucking closer to the bridge or even a pick if you don't use one.
Or try honing in on the problem area by reverting the amp to flat eq, and keep the volume down. Gradually turn up whilst the others are playing. When you reach a point where part of the sound cuts through too much, find it on the eq and reduce it (turn each eq knob up on its own, the problem area should jump out at you).
BTW, the contour on your amp cuts the mids and boosts the lows and highs, cranking this too much will kill your sound and add too much boom and clatter. I would only use this sparingly to tame any wild unpleasant mid range 'honk'.
There may also be a problem that the guitarists tone isn't gelling with yours. If the mix is sounding boomy, he will need to cut his low end to give you room, or conversely, he may need to add in low end to counteract your low end 'cutting through'.
