I've got a '96 170 TF (same boat with single console). If your's is set up like mine, the livewell is just an ON/OFF configuration. The few times that I've put bass in the livewell, I've just run the livewell a few minutes at a time every 30 minutes or so. There is supposed to be a "stand pipe" in the livewell that will keep water from coming in the livewell (you can pull the pipe out to fill the LW or run the livewell pump to fill it), but allow water to drain out should the level get over the top of the stand pipe. Mine didn't have the stand pipe, so I just put a plug in the drain if I need to keep water in it. If I don't put a plug in it, when I stop, water will enter the livewell and "find it's own level" (the water level in the livewell will be the same as the water level on the side of the boat). When under way, the water will drain out through the drain as the boat will be up on the pad and no water can get in the livewell. The stand pipe will keep the water from draining out when running. Hope that makes sense. If you do run the livewell pump manually, DO NOT forget to turn it off at the end of the day. Your battery will last longer than the pump if the pump is run dry...I learned that lesson the hard way. The pump will overheat and melt or crack, as it did in my old Stratos. I found that out when I saw water about ankle deep in the floor of the boat.
My bilge pump is also an ON/OFF configuration. I'll turn the bilge pump on every couple of hours to make sure no water has made its way into the bilge. About the only time I have had water in the bilge is when I stop and get a slight backwash over the transom.