VI,
For your water tank, pull the hose out of the fitting at the base of the tank. There should be a brain hole in the floor at the aft end of the Haitian hatch compartment. The water will drain into the bilge. After that, reattach the hose, pour some potable anti-freeze (the pink stuff) in your tank, turn on your pump to pressurize your system, spray the transom shower until you see pink, and you're good to go...
That tube simply is the garboard drain conduit, it's where the water in your bilge drains out of...
As far as your fishbox/rain issues, you can try putting some weather stripping on top of the gutter drain dam, but that won't help the small center section. It's held in place by 4 screws, you can remove those and put some of the stripping down, then screw them back in...
If your boat was built before May of '00, I built her. Got any pics of the wiring in the console? I'd love to see it...