Not sure how the 2005 Fisherman is set up and you mentioned live wells "plural". My 2006 Fisherman has one live well; behind the helm seat. Hatches up front with rubber stoppers are fish boxes with drains. For the live well to operate, you must open the seacock that is accessible through the deck plate directly in front of the motor splashguard. My live well doesn't use a drain tube; it has an overflow built into the live well that pushes the waste water out the top of the live well. To operate the well, open the seacock, put the black stopper in the BOTTOM drain then turn on the switch on the dash. The live well will start filling, the water will move in a circular motion and when it fills, the overflow/waste will go out through the top drain. I always operate mine with the stopper in, that way if you shut off the pump for any reason, the well won't drain when you are stopped.
When you are finished for the day, shut off the pump, pull the black stopper and let it drain then close the seacock. Make sure you net all the bait out before you pull the plug, or any small bait can get sucked into the bottom drain. I usually rinse mine a few times with fresh water a couple of times or it will start to stink!
Hope that helps.