An issue that I faced with water in bilge was the livewell overflowing, My issue was when i would run the fill pump (not the recirculating pump) it would fill faster than the water would exit through the little 1 inch overflow tube in hull, I ran a peice of weed eater string through the one inch overflow at the top of the livewell without any issues, the dang pump was just putting water in the livewell at a larger volume than it could easily get rid of.
The fix for me was to take the inlet jet and push it in further inside the well and restrict the flow from the fill pump just a little.
Hope this helps if this is indeed the issue. I had to adjust it until I could get the same rate of fill and overflow matched